diff --git a/.codespellrc b/.codespellrc index f95ef2dc7..1964710c8 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic* builtin = clear,rare -ignore-words-list = nd +ignore-words-list = nd,te diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index 019a4772b..55073f3a1 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -98,6 +98,11 @@ jobs: fi shell: bash + - name: Skip MRS validation for legacy validator + run: for DS in mrs_*; do touch $DS/.SKIP_VALIDATION; done + if: "matrix.bids-validator != 'master-deno'" + shell: bash + - name: Validate all BIDS datasets using bids-validator run: | cat ./run_tests.sh diff --git a/README.md b/README.md index ae75b5259..5fd612af7 100644 --- a/README.md +++ b/README.md @@ -174,12 +174,12 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------|:------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| -| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | -| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm’s general online tutorial | anat, meg | ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar) | -| [ds000247](https://github.com/bids-standard/bids-examples/tree/master/ds000247) | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat, meg | ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans | [link](https://openneuro.org/datasets/ds000247/versions/00001) | [@guiomar](https://github.com/guiomar) | -| [ds000248](https://github.com/bids-standard/bids-examples/tree/master/ds000248) | MNE sample data: Data with visual and auditory stimuli | anat, meg | FLASH, T1w, channels, coordsystem, events, meg, scans | [link](https://openneuro.org/datasets/ds000248/versions/00001) | [@agramfort](https://github.com/agramfort) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm’s general online tutorial | anat, meg | T1w, channels, coordsystem, headshape, meg, photo, scans | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar) | +| [ds000247](https://github.com/bids-standard/bids-examples/tree/master/ds000247) | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat, meg | T1w, channels, coordsystem, headshape, meg, scans | [link](https://openneuro.org/datasets/ds000247/versions/00001) | [@guiomar](https://github.com/guiomar) | +| [ds000248](https://github.com/bids-standard/bids-examples/tree/master/ds000248) | MNE sample data: Data with visual and auditory stimuli | anat, meg | FLASH, T1w, channels, coordsystem, events, meg, scans | [link](https://openneuro.org/datasets/ds000248/versions/00001) | [@agramfort](https://github.com/agramfort) | ### Microscopy @@ -188,13 +188,13 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------|:-----------------------------|:--------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------|:---------------------------------------------| -| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [micr_SEM](https://github.com/bids-standard/bids-examples/tree/master/micr_SEM) | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions | micr | SEM, photo, samples, sessions | [link](https://doi.org/10.5281/zenodo.5498378) | [@jcohenadad](https://github.com/jcohenadad) | -| [micr_SEMzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_SEMzarr) | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions | micr | SEM, SPIM, samples, sessions | n/a | [@TheChymera](https://github.com/TheChymera) | -| [micr_SPIM](https://github.com/bids-standard/bids-examples/tree/master/micr_SPIM) | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each | micr | SPIM, photo, samples | [link](https://doi.org/10.5281/zenodo.5517223) | [@jcohenadad](https://github.com/jcohenadad) | -| [micr_XPCTzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_XPCTzarr) | Example XPCT dataset in OME-ZARR format with 1 sample imaged | micr | XPCT, photo, samples, sessions | [link](https://human-organ-atlas.esrf.eu/datasets/572252538) | [@chourroutm](https://github.com/chourroutm) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------|:---------------------------------------------| +| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [micr_SEM](https://github.com/bids-standard/bids-examples/tree/master/micr_SEM) | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions | micr | SEM, photo, samples, sessions | [link](https://doi.org/10.5281/zenodo.5498378) | [@jcohenadad](https://github.com/jcohenadad) | +| [micr_SEMzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_SEMzarr) | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions | micr | SEM, SPIM, samples, sessions | n/a | [@TheChymera](https://github.com/TheChymera) | +| [micr_SPIM](https://github.com/bids-standard/bids-examples/tree/master/micr_SPIM) | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each | micr | SPIM, photo, samples | [link](https://doi.org/10.5281/zenodo.5517223) | [@jcohenadad](https://github.com/jcohenadad) | +| [micr_XPCTzarr](https://github.com/bids-standard/bids-examples/tree/master/micr_XPCTzarr) | Example XPCT dataset in OME-ZARR format with 1 sample imaged | micr | XPCT, photo, samples, sessions | [link](https://human-organ-atlas.esrf.eu/datasets/572252538) | [@chourroutm](https://github.com/chourroutm) | ### Motion @@ -203,12 +203,12 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:--------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------|:-----------------------------|:--------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:-------------------------------------------------| -| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask) | older and younger participants walking while performing discrimination task | eeg, motion | channels, eeg, events, motion, scans | n/a | [@sjeung](https://github.com/sjeung) | -| [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation) | participants rotated heading using full-body motion or joystick | eeg, motion | channels, coordsystem, eeg, electrodes, events, motion, scans | [link](https://openneuro.org/datasets/ds004460) | [@sjeung](https://github.com/sjeung) | -| [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation) | Example dataset of two different motion captured system recorded almost simultaneously, but no brain data | motion | channels, motion, scans | [link](https://doi.org/10.6084/m9.figshare.20238006.v2) | [@JuliusWelzel](https://github.com/JuliusWelzel) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:-------------------------------------------------| +| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask) | older and younger participants walking while performing discrimination task | eeg, motion | channels, eeg, events, motion, scans | n/a | [@sjeung](https://github.com/sjeung) | +| [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation) | participants rotated heading using full-body motion or joystick | eeg, motion | channels, coordsystem, eeg, electrodes, events, motion, scans | [link](https://openneuro.org/datasets/ds004460) | [@sjeung](https://github.com/sjeung) | +| [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation) | Example dataset of two different motion captured system recorded almost simultaneously, but no brain data | motion | channels, motion, scans | [link](https://doi.org/10.6084/m9.figshare.20238006.v2) | [@JuliusWelzel](https://github.com/JuliusWelzel) | ### MRI @@ -217,36 +217,49 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:--------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| -| [7t_trt](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) | n/a | anat, fmap, func | T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions | [link](https://bit.ly/2H0Z6Qt) | n/a | -| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | -| [ds001](https://github.com/bids-standard/bids-examples/tree/master/ds001) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000001/versions/00006) | n/a | -| [ds002](https://github.com/bids-standard/bids-examples/tree/master/ds002) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000002/versions/00002) | n/a | -| [ds003](https://github.com/bids-standard/bids-examples/tree/master/ds003) | single task, single run | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000003/versions/00001) | n/a | -| [ds005](https://github.com/bids-standard/bids-examples/tree/master/ds005) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000005/versions/00001) | n/a | -| [ds006](https://github.com/bids-standard/bids-examples/tree/master/ds006) | single task, multiple sessions, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000006/versions/00001) | n/a | -| [ds007](https://github.com/bids-standard/bids-examples/tree/master/ds007) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000007/versions/00001) | n/a | -| [ds008](https://github.com/bids-standard/bids-examples/tree/master/ds008) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000008/versions/00001) | n/a | -| [ds009](https://github.com/bids-standard/bids-examples/tree/master/ds009) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2, scans | [link](https://openneuro.org/datasets/ds000009/versions/00002) | n/a | -| [ds011](https://github.com/bids-standard/bids-examples/tree/master/ds011) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000011/versions/00001) | n/a | -| [ds051](https://github.com/bids-standard/bids-examples/tree/master/ds051) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000051/versions/00001) | n/a | -| [ds052](https://github.com/bids-standard/bids-examples/tree/master/ds052) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000052/versions/00001) | n/a | -| [ds101](https://github.com/bids-standard/bids-examples/tree/master/ds101) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000101/versions/00004) | n/a | -| [ds102](https://github.com/bids-standard/bids-examples/tree/master/ds102) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000102/versions/00001) | n/a | -| [ds105](https://github.com/bids-standard/bids-examples/tree/master/ds105) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000105/versions/00001) | n/a | -| [ds107](https://github.com/bids-standard/bids-examples/tree/master/ds107) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000107/versions/00001) | n/a | -| [ds108](https://github.com/bids-standard/bids-examples/tree/master/ds108) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000108/versions/00002) | n/a | -| [ds109](https://github.com/bids-standard/bids-examples/tree/master/ds109) | multiple tasks, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000109/versions/00001) | n/a | -| [ds110](https://github.com/bids-standard/bids-examples/tree/master/ds110) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000110/versions/00001) | n/a | -| [ds113b](https://github.com/bids-standard/bids-examples/tree/master/ds113b) | forrest gump watching, multiple sessions, multiple runs | func | bold, events | [link](https://openneuro.org/datasets/ds000113/versions/1.3.0) | n/a | -| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114) | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a | -| [ds116](https://github.com/bids-standard/bids-examples/tree/master/ds116) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000116/versions/00003) | n/a | -| [ds210](https://github.com/bids-standard/bids-examples/tree/master/ds210) | multiple tasks, multiple runs | func | bold, physio | [link](https://openneuro.org/datasets/ds000210/versions/00002) | n/a | -| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, eeg, func | T1w, bold, dwi, eeg | n/a | [@cpernet](https://github.com/cpernet) | -| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) | -| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | -| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------| +| [7t_trt](https://github.com/bids-standard/bids-examples/tree/master/7t_trt) | n/a | anat, fmap, func | T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions | [link](https://bit.ly/2H0Z6Qt) | n/a | +| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [ds001](https://github.com/bids-standard/bids-examples/tree/master/ds001) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000001/versions/00006) | n/a | +| [ds002](https://github.com/bids-standard/bids-examples/tree/master/ds002) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000002/versions/00002) | n/a | +| [ds003](https://github.com/bids-standard/bids-examples/tree/master/ds003) | single task, single run | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000003/versions/00001) | n/a | +| [ds005](https://github.com/bids-standard/bids-examples/tree/master/ds005) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000005/versions/00001) | n/a | +| [ds006](https://github.com/bids-standard/bids-examples/tree/master/ds006) | single task, multiple sessions, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000006/versions/00001) | n/a | +| [ds007](https://github.com/bids-standard/bids-examples/tree/master/ds007) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000007/versions/00001) | n/a | +| [ds008](https://github.com/bids-standard/bids-examples/tree/master/ds008) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000008/versions/00001) | n/a | +| [ds009](https://github.com/bids-standard/bids-examples/tree/master/ds009) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2, scans | [link](https://openneuro.org/datasets/ds000009/versions/00002) | n/a | +| [ds011](https://github.com/bids-standard/bids-examples/tree/master/ds011) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000011/versions/00001) | n/a | +| [ds051](https://github.com/bids-standard/bids-examples/tree/master/ds051) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000051/versions/00001) | n/a | +| [ds052](https://github.com/bids-standard/bids-examples/tree/master/ds052) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000052/versions/00001) | n/a | +| [ds101](https://github.com/bids-standard/bids-examples/tree/master/ds101) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000101/versions/00004) | n/a | +| [ds102](https://github.com/bids-standard/bids-examples/tree/master/ds102) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000102/versions/00001) | n/a | +| [ds105](https://github.com/bids-standard/bids-examples/tree/master/ds105) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000105/versions/00001) | n/a | +| [ds107](https://github.com/bids-standard/bids-examples/tree/master/ds107) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000107/versions/00001) | n/a | +| [ds108](https://github.com/bids-standard/bids-examples/tree/master/ds108) | single task, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000108/versions/00002) | n/a | +| [ds109](https://github.com/bids-standard/bids-examples/tree/master/ds109) | multiple tasks, multiple runs | anat, func | T1w, bold, events | [link](https://openneuro.org/datasets/ds000109/versions/00001) | n/a | +| [ds110](https://github.com/bids-standard/bids-examples/tree/master/ds110) | single task, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000110/versions/00001) | n/a | +| [ds113b](https://github.com/bids-standard/bids-examples/tree/master/ds113b) | forrest gump watching, multiple sessions, multiple runs | func | bold, events | [link](https://openneuro.org/datasets/ds000113/versions/1.3.0) | n/a | +| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114) | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a | +| [ds116](https://github.com/bids-standard/bids-examples/tree/master/ds116) | multiple tasks, multiple runs | anat, func | T1w, bold, events, inplaneT2 | [link](https://openneuro.org/datasets/ds000116/versions/00003) | n/a | +| [ds210](https://github.com/bids-standard/bids-examples/tree/master/ds210) | multiple tasks, multiple runs | func | bold, physio | [link](https://openneuro.org/datasets/ds000210/versions/00002) | n/a | +| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | anat, dwi, eeg, func | T1w, bold, dwi, eeg | n/a | [@cpernet](https://github.com/cpernet) | +| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) | +| [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | [@irisgroen](https://github.com/irisgroen) | +| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) | + +### MRS + + + +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------|:------------|:-------------------------|:-------------------------------------------------|:---------------------------------------------------| +| [mrs_2dmrsi](https://github.com/bids-standard/bids-examples/tree/master/mrs_2dmrsi) | 2D sLASER MRSI data from 8 subjects | anat, mrs | T1w, mrsi | [link](https://zenodo.org/records/7701228) | [@markmikkelsen](https://github.com/markmikkelsen) | +| [mrs_biggaba](https://github.com/bids-standard/bids-examples/tree/master/mrs_biggaba) | MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project | anat, mrs | T1w, mrsref, svs | [link](https://www.nitrc.org/projects/biggaba) | [@markmikkelsen](https://github.com/markmikkelsen) | +| [mrs_fmrs](https://github.com/bids-standard/bids-examples/tree/master/mrs_fmrs) | Functional MRS data involving a pain stimulus task from 15 subjects | anat, mrs | T1w, events, mrsref, svs | [link](https://www.nitrc.org/projects/fmrs_2020) | [@markmikkelsen](https://github.com/markmikkelsen) | ### NIRS @@ -303,8 +316,8 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:--------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------| -| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | -| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | -| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------| +| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) | +| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) | +| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) | diff --git a/dataset_listing.tsv b/dataset_listing.tsv index 78f77c222..f3540c073 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -2,7 +2,7 @@ name description link to full data maintained by datatypes suffixes eeg_matchingpennies Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) [link](https://doi.org/10.17605/OSF.IO/CJ2DR) [@sappelhoff](https://github.com/sappelhoff) eeg channels, eeg, events eeg_rishikesh Mind wandering experiment. EEG data in Biosemi (.bdf) format [link](https://openneuro.org/datasets/ds001787) [@arnodelorme](https://github.com/arnodelorme) eeg channels, eeg, events eeg_face13 Deconstructing the early visual electrocortical response to face and house stimuli. EDF format [@andesha](https://github.com/andesha) eeg channels, coordsystem, eeg, electrodes, events -eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans +eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans eeg_ds003645s_hed_library HED annotation using HED library vocabularies (schema). [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) eeg channels, eeg, events eeg_cbm Rest EEG. European Data Format (.edf) [@cpernet](https://github.com/cpernet) eeg channels, eeg, events, scans ieeg_filtered_speech recordings of three seizures [@choldgraf](https://github.com/choldgraf) ieeg channels, coordsystem, electrodes, events, ieeg, photo @@ -63,9 +63,9 @@ micr_XPCTzarr Example XPCT dataset in OME-ZARR format with 1 sample imaged [link fnirs_tapping Example fNIRS measurement with three conditions from five subjects [link](https://doi.org/10.5281/zenodo.5529797) [@rob-luke](https://github.com/rob-luke) nirs channels, coordsystem, events, nirs, optodes, scans fnirs_automaticity 24 subjects performing (non-)automatic finger tapping and foot stepping [link](https://doi.org/10.34973/vesb-mh30) [@robertoostenveld](https://github.com/robertoostenveld) nirs channels, coordsystem, events, nirs, optodes, practicelogbook, scans motion_systemvalidation Example dataset of two different motion captured system recorded almost simultaneously, but no brain data [link](https://doi.org/10.6084/m9.figshare.20238006.v2) [@JuliusWelzel](https://github.com/JuliusWelzel) motion channels, motion, scans -ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task [link](https://openneuro.org/datasets/ds000117/) [@RikHenson](https://github.com/RikHenson) anat, beh, dwi, fmap, func, meg FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans -ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans -ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans +ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task [link](https://openneuro.org/datasets/ds000117/) [@RikHenson](https://github.com/RikHenson) anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans +ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, photo, scans +ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, scans ds000248 MNE sample data: Data with visual and auditory stimuli [link](https://openneuro.org/datasets/ds000248/versions/00001) [@agramfort](https://github.com/agramfort) anat, meg FLASH, T1w, channels, coordsystem, events, meg, scans eeg_ds000117 Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) [link](https://openneuro.org/datasets/ds000117/) [@robertoostenveld](https://github.com/robertoostenveld) anat, eeg T1w, channels, coordsystem, eeg, electrodes, events eeg_rest_fmri Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) [@cpernet](https://github.com/cpernet) anat, dwi, eeg, func T1w, bold, dwi, eeg @@ -76,3 +76,6 @@ ieeg_visual_multimodal [@irisgroen](https://github.com/irisgroen) anat, fmap, genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, func FLAIR, T1w, bold, dwi, events, info motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans motion_spotrotation participants rotated heading using full-body motion or joystick [link](https://openneuro.org/datasets/ds004460) [@sjeung](https://github.com/sjeung) eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans +mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsi +mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project [link](https://www.nitrc.org/projects/biggaba) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsref, svs +mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [link](https://www.nitrc.org/projects/fmrs_2020) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, events, mrsref, svs diff --git a/mrs_2dmrsi/CHANGES b/mrs_2dmrsi/CHANGES new file mode 100644 index 000000000..f13284bbf --- /dev/null +++ b/mrs_2dmrsi/CHANGES @@ -0,0 +1,5 @@ +1.0.1 2023-11-28 + - Edits for inclusion into https://github.com/bids-standard/bids-examples + +1.0.0 2022-10-06 + - Initial release diff --git a/mrs_2dmrsi/README.md b/mrs_2dmrsi/README.md new file mode 100644 index 000000000..24a74158e --- /dev/null +++ b/mrs_2dmrsi/README.md @@ -0,0 +1,31 @@ +# 2D semi-LASER MRSI reproducibility dataset + +Contact: + +Data availability: + +Publications: + +- + +## Overview + +The data from this study were acquired as part of a project to validate [SLIPMAT](https://doi.org/10.1016/j.neuroimage.2023.120235), a tool to extract high-quality, tissue-specific, spectral profiles from MR spectroscopic imaging data (MRSI). + +Data types included are T1-weighted structural MRI images and 2D semi-LASER MRSI data. Each subject has three runs of each MRSI acquisition. + +## Methods + +### Subjects + +Eight healthy adults (2 females, 6 males, mean age = 21 years). + +### MR protocol + +Reproduced with slight modifications from [SLIPMAT](https://doi.org/10.1016/j.neuroimage.2023.120235): + +MR data were acquired using a 3T Siemens Magnetom Prisma (Siemens Healthcare, Erlangen, Germany) system using a 32-channel receiver head coil-array. A T1-weighted MRI scan was acquired with a 3D-MPRAGE sequence: FOV = 208 × 256 × 256 mm, resolution = 1 × 1 × 1 mm3, TE / TR = 2 ms / 2000 ms, inversion time = 880 ms, flip angle = 8°, GRAPPA acceleration factor = 2, 4 min 54 s scan duration. Water suppressed MRSI data were acquired with 2D phase-encoding: FOV = 160 × 160 × 15 mm3, nominal voxel resolution 10 × 10 × 15 mm3, TE / TR = 40 ms / 2000 ms, complex data points = 1024, sampling frequency = 2000 Hz. The MRSI slice was aligned axially in the subcallosal plane with an approximately 1 mm gap from the upper surface of the corpus callosum. The semi-LASER method ([Scheenen et al., 2008](https://doi.org/10.1002/mrm.21302)) was used localize a 100 × 100 × 15 mm VOI, central to the FOV, four saturation regions were placed around the VOI prescribing a 100 × 100 mm interior, and an additional four saturation regions were positioned to intersect the four corners of the semi-LASER VOI to provide additional scalp lipid suppression. The total acquisition time for a single MRSI scan was 5 min and 6 s, and three MRSI datasets were acquired sequentially during the same session to assess technical repeatability. + +### Experimental location + +Centre for Human Brain Health, University of Birmingham, Birmingham, UK. diff --git a/mrs_2dmrsi/dataset_description.json b/mrs_2dmrsi/dataset_description.json new file mode 100644 index 000000000..d7ac01487 --- /dev/null +++ b/mrs_2dmrsi/dataset_description.json @@ -0,0 +1,21 @@ +{ + "Name": "mrs_2dmrsi", + "BIDSVersion": "1.10.0", + "DatasetType": "raw", + "License": "Creative Commons Attribution 4.0 International License", + "Authors": [ + "Martin Wilson", + "Olivia Vella" + ], + "ReferencesAndLinks": [ + "doi:10.1016/j.neuroimage.2023.120235" + ], + "DatasetDOI": "doi:10.5281/zenodo.7701228", + "SourceDatasets": [ + { + "URL": "https://zenodo.org/records/7701228", + "DOI": "doi:10.5281/zenodo.7701228", + "Version": "v4" + } + ] +} diff --git a/mrs_2dmrsi/sub-01/anat/sub-01_T1w.json b/mrs_2dmrsi/sub-01/anat/sub-01_T1w.json new file mode 100644 index 000000000..3b6a87a6f --- /dev/null +++ b/mrs_2dmrsi/sub-01/anat/sub-01_T1w.json @@ -0,0 +1,72 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.252, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "CHBH", + "InstitutionalDepartmentName": "CHBH", + "InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA", + "DeviceSerialNumber": "166100", + "StationName": "AWP166100", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "T1_vol_MPR_v1", + "ProtocolName": "T1_vol_MPR_v1", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SK\\SP\\MP\\OSP", + "ScanOptions": "IR", + "SequenceName": "*tfl3d1_16ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 7, + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0560902, + "EchoTime": 0.00203, + "RepetitionTime": 2, + "SpoilingState": true, + "InversionTime": 0.88, + "FlipAngle": 8, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + -6825, + -3922, + 3512, + 392, + -104, + -143, + 93, + 30 ], + "TxRefAmp": 252.801, + "PhaseResolution": 1, + "PhaseOversampling": 0.05, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%SiemensSeq%\\tfl", + "RefLinesPE": 24, + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "MatrixCoilMode": "GRAPPA", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 269, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 240, + "DwellTime": 8.2e-06, + "ImageOrientationPatientDICOM": [ + -0.0456605, + 0.996282, + 0.0730621, + 0.00408772, + 0.0733241, + -0.9973 ], + "ImageOrientationText": "Sag>Cor(-2.6)>Tra(-0.4)", + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20211006" +} diff --git a/mrs_2dmrsi/sub-01/anat/sub-01_T1w.nii.gz b/mrs_2dmrsi/sub-01/anat/sub-01_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.json b/mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.json new file mode 100644 index 000000000..fbcfbb1c1 --- /dev/null +++ b/mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252145], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.nii.gz b/mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.json b/mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.json new file mode 100644 index 000000000..fbcfbb1c1 --- /dev/null +++ b/mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252145], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.nii.gz b/mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.json b/mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.json new file mode 100644 index 000000000..fbcfbb1c1 --- /dev/null +++ b/mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252145], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.nii.gz b/mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-02/anat/sub-02_T1w.json b/mrs_2dmrsi/sub-02/anat/sub-02_T1w.json new file mode 100644 index 000000000..138b8725f --- /dev/null +++ b/mrs_2dmrsi/sub-02/anat/sub-02_T1w.json @@ -0,0 +1,72 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.252, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "CHBH", + "InstitutionalDepartmentName": 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b/mrs_2dmrsi/sub-05/mrs/sub-05_run-2_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-05/mrs/sub-05_run-3_mrsi.json b/mrs_2dmrsi/sub-05/mrs/sub-05_run-3_mrsi.json new file mode 100644 index 000000000..0b3fe65ed --- /dev/null +++ b/mrs_2dmrsi/sub-05/mrs/sub-05_run-3_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252131], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-05/mrs/sub-05_run-3_mrsi.nii.gz b/mrs_2dmrsi/sub-05/mrs/sub-05_run-3_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-06/anat/sub-06_T1w.json b/mrs_2dmrsi/sub-06/anat/sub-06_T1w.json new file mode 100644 index 000000000..854cecf65 --- /dev/null +++ b/mrs_2dmrsi/sub-06/anat/sub-06_T1w.json @@ -0,0 +1,72 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.252, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "CHBH", + "InstitutionalDepartmentName": "CHBH", + "InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA", + "DeviceSerialNumber": "166100", + "StationName": "AWP166100", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "T1_vol_MPR_v1", + "ProtocolName": "T1_vol_MPR_v1", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SK\\SP\\MP\\OSP", + "ScanOptions": "IR", + "SequenceName": "*tfl3d1_16ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 7, + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0501916, + "EchoTime": 0.00203, + "RepetitionTime": 2, + "SpoilingState": true, + "InversionTime": 0.88, + 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b/mrs_2dmrsi/sub-06/mrs/sub-06_run-2_mrsi.json new file mode 100644 index 000000000..28e59f715 --- /dev/null +++ b/mrs_2dmrsi/sub-06/mrs/sub-06_run-2_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252122], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-06/mrs/sub-06_run-2_mrsi.nii.gz b/mrs_2dmrsi/sub-06/mrs/sub-06_run-2_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-06/mrs/sub-06_run-3_mrsi.json b/mrs_2dmrsi/sub-06/mrs/sub-06_run-3_mrsi.json new file mode 100644 index 000000000..28e59f715 --- /dev/null +++ b/mrs_2dmrsi/sub-06/mrs/sub-06_run-3_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252122], + "ResonantNucleus": ["1H"], + 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"ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "MatrixCoilMode": "GRAPPA", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 269, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 240, + "DwellTime": 8.2e-06, + "ImageOrientationPatientDICOM": [ + -0.00850693, + 0.993667, + 0.112043, + -0.0475121, + 0.111518, + -0.992626 ], + "ImageOrientationText": "Sag>Tra(2.7)>Cor(-0.8)", + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20211006" +} diff --git a/mrs_2dmrsi/sub-07/anat/sub-07_T1w.nii.gz b/mrs_2dmrsi/sub-07/anat/sub-07_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-1_mrsi.json b/mrs_2dmrsi/sub-07/mrs/sub-07_run-1_mrsi.json new file mode 100644 index 000000000..307c88d97 --- /dev/null +++ b/mrs_2dmrsi/sub-07/mrs/sub-07_run-1_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252075], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-1_mrsi.nii.gz b/mrs_2dmrsi/sub-07/mrs/sub-07_run-1_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-2_mrsi.json b/mrs_2dmrsi/sub-07/mrs/sub-07_run-2_mrsi.json new file mode 100644 index 000000000..307c88d97 --- /dev/null +++ b/mrs_2dmrsi/sub-07/mrs/sub-07_run-2_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252075], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-2_mrsi.nii.gz b/mrs_2dmrsi/sub-07/mrs/sub-07_run-2_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-3_mrsi.json b/mrs_2dmrsi/sub-07/mrs/sub-07_run-3_mrsi.json new file mode 100644 index 000000000..307c88d97 --- /dev/null +++ b/mrs_2dmrsi/sub-07/mrs/sub-07_run-3_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252075], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-07/mrs/sub-07_run-3_mrsi.nii.gz b/mrs_2dmrsi/sub-07/mrs/sub-07_run-3_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-08/anat/sub-08_T1w.json b/mrs_2dmrsi/sub-08/anat/sub-08_T1w.json new file mode 100644 index 000000000..e550734c1 --- /dev/null +++ b/mrs_2dmrsi/sub-08/anat/sub-08_T1w.json @@ -0,0 +1,72 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.252, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "CHBH", + "InstitutionalDepartmentName": "CHBH", + "InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA", + "DeviceSerialNumber": "166100", + "StationName": "AWP166100", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "T1_vol_MPR_v1", + "ProtocolName": "T1_vol_MPR_v1", + "ScanningSequence": "GR\\IR", + "SequenceVariant": "SK\\SP\\MP\\OSP", + "ScanOptions": "IR", + "SequenceName": "*tfl3d1_16ns", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 10, + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.05305, + "EchoTime": 0.00203, + "RepetitionTime": 2, + "SpoilingState": true, + "InversionTime": 0.88, + "FlipAngle": 8, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + -6833, + -3891, + 3561, + 294, + -63, + -118, + -14, + -6 ], + "TxRefAmp": 257.307, + "PhaseResolution": 1, + "PhaseOversampling": 0.05, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%SiemensSeq%\\tfl", + "RefLinesPE": 24, + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "MatrixCoilMode": "GRAPPA", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 269, + "AcquisitionMatrixPE": 256, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 2, + "PixelBandwidth": 240, + "DwellTime": 8.2e-06, + "ImageOrientationPatientDICOM": [ + -0.0438541, + 0.997371, + -0.0576951, + 0.0412026, + -0.0558959, + -0.997586 ], + "ImageOrientationText": "Sag>Cor(-2.6)>Tra(-2.2)", + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20211006" +} diff --git a/mrs_2dmrsi/sub-08/anat/sub-08_T1w.nii.gz b/mrs_2dmrsi/sub-08/anat/sub-08_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-1_mrsi.json b/mrs_2dmrsi/sub-08/mrs/sub-08_run-1_mrsi.json new file mode 100644 index 000000000..dee157aa9 --- /dev/null +++ b/mrs_2dmrsi/sub-08/mrs/sub-08_run-1_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252034], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-1_mrsi.nii.gz b/mrs_2dmrsi/sub-08/mrs/sub-08_run-1_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-2_mrsi.json b/mrs_2dmrsi/sub-08/mrs/sub-08_run-2_mrsi.json new file mode 100644 index 000000000..dee157aa9 --- /dev/null +++ b/mrs_2dmrsi/sub-08/mrs/sub-08_run-2_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252034], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-2_mrsi.nii.gz b/mrs_2dmrsi/sub-08/mrs/sub-08_run-2_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-3_mrsi.json b/mrs_2dmrsi/sub-08/mrs/sub-08_run-3_mrsi.json new file mode 100644 index 000000000..dee157aa9 --- /dev/null +++ b/mrs_2dmrsi/sub-08/mrs/sub-08_run-3_mrsi.json @@ -0,0 +1,13 @@ +{ + "SpectrometerFrequency": [123.252034], + "ResonantNucleus": ["1H"], + "SpectralWidth": 2000, + "NumberOfSpectralPoints": 1024, + "AcquisitionVoxelSize": [10, 10, 15], + "ChemicalShiftOffset": 4.65, + "EchoTime": 0.04, + "RepetitionTime": 2, + "FlipAngle": 90, + "SequenceName": "%SiemensSeq%\\csi_slaser", + "ChemicalShiftReference": 2 +} diff --git a/mrs_2dmrsi/sub-08/mrs/sub-08_run-3_mrsi.nii.gz b/mrs_2dmrsi/sub-08/mrs/sub-08_run-3_mrsi.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/README.md b/mrs_biggaba/README.md new file mode 100644 index 000000000..103ba499c --- /dev/null +++ b/mrs_biggaba/README.md @@ -0,0 +1,59 @@ +# Big GABA + +Contact: + +Data availability: + +Publications: + +- +- +- + +## Overview + +These data were acquired as part of the Big GABA project, a large-scale multi-site study to determine differences in the measurement outcomes from GABA-edited and non-edited single-voxel MRS data across the three major MRI manufacturers: GE, Philips, and Siemens. The data here are only from one site (P3). Please visit the [Big GABA data repository](https://www.nitrc.org/projects/biggaba/) and refer to the publications above for more information. + +Data types included are T1-weighted structural MRI images and single-voxel PRESS and GABA-edited MEGA-PRESS MRS data. The MEGA-PRESS data were acquired using standard GABA editing (TE = 68 ms) and symmetric macromolecule suppression (TE = 80 ms). + +## Methods + +### Subjects + +Twelve healthy adults (7 males, 5 females, mean age = 29 years). + +### MR protocol + +MR data were acquired using a 3T Philips Achieva (Philips Healthcare, Eindhoven, Netherlands) system using a body coil for transmit and a 32-channel phased-array head coil for receive. + +#### MRI + +T1-weighted structural MRI acquisition parameters: + +- Voxel resolution = 1 × 1 × 1 mm3 +- TE/TI/TR (ms) = 3.1/865/6.9 +- Scan duration = 7 min 10 s +- Flip angle = 8° +- Slices = 204 +- FOV = 256 × 256 mm2 +- Matrix size = 256 × 256 × 204 +- SENSE acceleration factor = 2 + +#### MRS + +General MRS acquisition parameters: + +- Volume of interest = medial parietal lobe +- Voxel resolution = 30 × 30 × 30 mm3 +- Spectral width = 2000 Hz +- Number of points = 2048 + +##### PRESS + +- TE/TR = 35/2000 ms +- Number of transients = 64 + +##### MEGA-PRESS + +- TE/TR = 68 (for standard GABA editing) or 80 (for symmetric macromolecule suppression)/2000 ms +- Number of transients = 320 diff --git a/mrs_biggaba/dataset_description.json b/mrs_biggaba/dataset_description.json new file mode 100644 index 000000000..47e3a54b1 --- /dev/null +++ b/mrs_biggaba/dataset_description.json @@ -0,0 +1,24 @@ +{ + "Name": "mrs_biggaba", + "BIDSVersion": "1.10.0", + "DatasetType": "raw", + "License": "Creative Commons Attribution-NonCommercial 4.0 International License", + "Authors": [ + "Mikkelsen et al." + ], + "Funding": [ + "NIH grant R01 EB016089" + ], + "ReferencesAndLinks": [ + "doi:10.1016/j.neuroimage.2017.07.021", + "doi:10.1016/j.neuroimage.2019.02.059", + "doi:10.1148/radiol.2020191037" + ], + "DatasetDOI": "doi:10.25790/bml0cm.78", + "SourceDatasets": [ + { + "URL": "https://www.nitrc.org/projects/biggaba/", + "DOI": "doi:10.25790/bml0cm.78" + } + ] +} \ No newline at end of file diff --git a/mrs_biggaba/participants.json b/mrs_biggaba/participants.json new file mode 100755 index 000000000..d039ecee0 --- /dev/null +++ b/mrs_biggaba/participants.json @@ -0,0 +1,16 @@ +{ + "participant_id": { + "Description": "Unique participant identifier" + }, + "sex": { + "Description": "Sex of the participant", + "Levels": { + "M": "Male", + "F": "Female" + } + }, + "age": { + "Description": "Age of the participant", + "Units": "years" + } +} diff --git a/mrs_biggaba/participants.tsv b/mrs_biggaba/participants.tsv new file mode 100644 index 000000000..4e1119e63 --- /dev/null +++ b/mrs_biggaba/participants.tsv @@ -0,0 +1,13 @@ +participant_id sex age +sub-01 M 31 +sub-02 M 29 +sub-03 M 31 +sub-04 F 27 +sub-05 F 27 +sub-06 M 28 +sub-07 M 33 +sub-08 F 25 +sub-09 M 32 +sub-10 F 24 +sub-11 M 30 +sub-12 F 34 \ No newline at end of file diff --git a/mrs_biggaba/sub-01/anat/sub-01_T1w.json b/mrs_biggaba/sub-01/anat/sub-01_T1w.json new file mode 100644 index 000000000..db67de3e3 --- /dev/null +++ b/mrs_biggaba/sub-01/anat/sub-01_T1w.json @@ -0,0 +1,17 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SENSE", + "EchoTime": 0.00313, + "InversionTime": 0.865, + "RepetitionTimeExcitation": 0.006953, + "FlipAngle": 8, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe" +} diff --git a/mrs_biggaba/sub-01/anat/sub-01_T1w.nii.gz b/mrs_biggaba/sub-01/anat/sub-01_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_mrsref.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_mrsref.json new file mode 100644 index 000000000..d90bcd621 --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_mrsref.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_svs.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_svs.json new file mode 100644 index 000000000..6e1e0303e --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 15 + }, + "OFF": { + "FrequencyOffset": 7.46, + "PulseDuration": 15 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_svs.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress68_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_mrsref.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_mrsref.json new file mode 100644 index 000000000..9fe9ef094 --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_mrsref.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_svs.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_svs.json new file mode 100644 index 000000000..56f1012ac --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 20 + }, + "OFF": { + "FrequencyOffset": 1.5, + "PulseDuration": 20 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_svs.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-megapress80_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-press_mrsref.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_mrsref.json new file mode 100644 index 000000000..dc310339a --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-press_mrsref.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-press_svs.json b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_svs.json new file mode 100644 index 000000000..de0606ec9 --- /dev/null +++ b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_svs.json @@ -0,0 +1,25 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-01/mrs/sub-01_acq-press_svs.nii.gz b/mrs_biggaba/sub-01/mrs/sub-01_acq-press_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/anat/sub-02_T1w.json b/mrs_biggaba/sub-02/anat/sub-02_T1w.json new file mode 100644 index 000000000..db67de3e3 --- /dev/null +++ b/mrs_biggaba/sub-02/anat/sub-02_T1w.json @@ -0,0 +1,17 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SENSE", + "EchoTime": 0.00313, + "InversionTime": 0.865, + "RepetitionTimeExcitation": 0.006953, + "FlipAngle": 8, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe" +} diff --git a/mrs_biggaba/sub-02/anat/sub-02_T1w.nii.gz b/mrs_biggaba/sub-02/anat/sub-02_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_mrsref.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_mrsref.json new file mode 100644 index 000000000..d90bcd621 --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_mrsref.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_svs.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_svs.json new file mode 100644 index 000000000..6e1e0303e --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 15 + }, + "OFF": { + "FrequencyOffset": 7.46, + "PulseDuration": 15 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_svs.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress68_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_mrsref.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_mrsref.json new file mode 100644 index 000000000..9fe9ef094 --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_mrsref.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_svs.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_svs.json new file mode 100644 index 000000000..56f1012ac --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 20 + }, + "OFF": { + "FrequencyOffset": 1.5, + "PulseDuration": 20 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_svs.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-megapress80_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-press_mrsref.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_mrsref.json new file mode 100644 index 000000000..dc310339a --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-press_mrsref.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-press_svs.json b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_svs.json new file mode 100644 index 000000000..de0606ec9 --- /dev/null +++ b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_svs.json @@ -0,0 +1,25 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-02/mrs/sub-02_acq-press_svs.nii.gz b/mrs_biggaba/sub-02/mrs/sub-02_acq-press_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-03/anat/sub-03_T1w.json b/mrs_biggaba/sub-03/anat/sub-03_T1w.json new file mode 100644 index 000000000..db67de3e3 --- /dev/null +++ b/mrs_biggaba/sub-03/anat/sub-03_T1w.json @@ -0,0 +1,17 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SENSE", + "EchoTime": 0.00313, + "InversionTime": 0.865, + "RepetitionTimeExcitation": 0.006953, + "FlipAngle": 8, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe" +} diff --git a/mrs_biggaba/sub-03/anat/sub-03_T1w.nii.gz b/mrs_biggaba/sub-03/anat/sub-03_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-03/mrs/sub-03_acq-megapress68_mrsref.json b/mrs_biggaba/sub-03/mrs/sub-03_acq-megapress68_mrsref.json new file mode 100644 index 000000000..d90bcd621 --- /dev/null +++ b/mrs_biggaba/sub-03/mrs/sub-03_acq-megapress68_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", 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000000000..6e1e0303e --- /dev/null +++ b/mrs_biggaba/sub-03/mrs/sub-03_acq-megapress68_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 15 + }, + "OFF": { + "FrequencyOffset": 7.46, + "PulseDuration": 15 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + 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--git a/mrs_biggaba/sub-04/mrs/sub-04_acq-megapress80_svs.json b/mrs_biggaba/sub-04/mrs/sub-04_acq-megapress80_svs.json new file mode 100644 index 000000000..56f1012ac --- /dev/null +++ b/mrs_biggaba/sub-04/mrs/sub-04_acq-megapress80_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 20 + }, + "OFF": { + "FrequencyOffset": 1.5, + "PulseDuration": 20 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + 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index 000000000..dc310339a --- /dev/null +++ b/mrs_biggaba/sub-09/mrs/sub-09_acq-press_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-09/mrs/sub-09_acq-press_mrsref.nii.gz b/mrs_biggaba/sub-09/mrs/sub-09_acq-press_mrsref.nii.gz new file mode 100644 index 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b/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress68_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 15 + }, + "OFF": { + "FrequencyOffset": 7.46, + "PulseDuration": 15 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress68_svs.nii.gz b/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress68_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress80_mrsref.json b/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress80_mrsref.json new file mode 100644 index 000000000..9fe9ef094 --- /dev/null +++ b/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress80_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": 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"EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 20 + }, + "OFF": { + "FrequencyOffset": 1.5, + "PulseDuration": 20 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress80_svs.nii.gz b/mrs_biggaba/sub-11/mrs/sub-11_acq-megapress80_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-press_mrsref.json b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_mrsref.json new file mode 100644 index 000000000..dc310339a --- /dev/null +++ b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-press_mrsref.nii.gz b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-press_svs.json b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_svs.json new file mode 100644 index 000000000..de0606ec9 --- /dev/null +++ b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_svs.json @@ -0,0 +1,25 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-11/mrs/sub-11_acq-press_svs.nii.gz b/mrs_biggaba/sub-11/mrs/sub-11_acq-press_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/anat/sub-12_T1w.json b/mrs_biggaba/sub-12/anat/sub-12_T1w.json new file mode 100644 index 000000000..db67de3e3 --- /dev/null +++ b/mrs_biggaba/sub-12/anat/sub-12_T1w.json @@ -0,0 +1,17 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SENSE", + "EchoTime": 0.00313, + "InversionTime": 0.865, + "RepetitionTimeExcitation": 0.006953, + "FlipAngle": 8, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe" +} diff --git a/mrs_biggaba/sub-12/anat/sub-12_T1w.nii.gz b/mrs_biggaba/sub-12/anat/sub-12_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_mrsref.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_mrsref.json new file mode 100644 index 000000000..d90bcd621 --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_mrsref.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_svs.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_svs.json new file mode 100644 index 000000000..6e1e0303e --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.068, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 15 + }, + "OFF": { + "FrequencyOffset": 7.46, + "PulseDuration": 15 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_svs.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress68_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_mrsref.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_mrsref.json new file mode 100644 index 000000000..9fe9ef094 --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_mrsref.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_svs.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_svs.json new file mode 100644 index 000000000..56f1012ac --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_svs.json @@ -0,0 +1,37 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "MEGA-PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.08, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "EditTarget": "GABA", + "EditPulse": { + "ON": { + "FrequencyOffset": 1.9, + "PulseDuration": 20 + }, + "OFF": { + "FrequencyOffset": 1.5, + "PulseDuration": 20 + } + }, + "EditCondition": ["ON", "OFF"], + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_svs.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-megapress80_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-press_mrsref.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_mrsref.json new file mode 100644 index 000000000..dc310339a --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_mrsref.json @@ -0,0 +1,24 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 8, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": false, + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 4.68, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-press_mrsref.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-press_svs.json b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_svs.json new file mode 100644 index 000000000..de0606ec9 --- /dev/null +++ b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_svs.json @@ -0,0 +1,25 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "SoftwareVersions": "R3.2.2", + "MagneticFieldStrength": 3, + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.751], + "SpectralWidth": 2000, + "EchoTime": 0.035, + "NumberOfSpectralPoints": 2048, + "NumberOfTransients": 320, + "RepetitionTime": 2, + "AcquisitionVoxelSize": [30, 30, 30], + "BodyPart": "BRAIN", + "BodyPartDetails": "Medial parietal lobe", + "WaterSuppression": true, + "WaterSuppressionTechnique": "VAPOR", + "OuterVolumeSuppression": false, + "B0ShimmingTechnique": "Second-order pencil-beam projection", + "ChemicalShiftOffset": 4.68, + "ChemicalShiftReference": 3, + "EchoAcquisition": "Half echo" +} diff --git a/mrs_biggaba/sub-12/mrs/sub-12_acq-press_svs.nii.gz b/mrs_biggaba/sub-12/mrs/sub-12_acq-press_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/README.md b/mrs_fmrs/README.md new file mode 100644 index 000000000..09c00f871 --- /dev/null +++ b/mrs_fmrs/README.md @@ -0,0 +1,31 @@ +# fMRS in Pain + +Contact: + +Data availability: + +Publications: + +- + +## Dataset Description + +This dataset includes anatomical and functional MRS data for 15 participants (see demographics in participants.tsv). +The data were collected using a 3T Philips Achieva scanner (Best, Netherlands) with a +single-channel transmit-receive head coil, using the PRESS sequence. + +Baseline: TE/TR = 22/4000 ms, NSA = 32, scan time = 3:12 min, and 16 non-water suppressed spectra were acquired. + +Functional: TE/TR = 22/4000 ms, NSA = 16, scan time = 22:40 min; ACC voxel size = 30 × 25 × 15 mm3, second-order shimming, 16-step phase cycle with water suppression using the excitation option – a Philips variant of CHESS; a non-water suppressed acquisition preceded each complete phase-cycle for absolute metabolite quantification and water signal monitoring. + +The during the functional MRS scan participants had capsaicin cream on the forearm for the entire duration, and heat was applied for 4 min after 8 min of data collection, which corresponds to shots 128-192. + +## Stimulation Paradigm + +The pain model consisted of the application of 0.075% topical capsaicin and heat activation via a thermo-pad on the volar surface of the right forearm (~8 × 5 cm2). Capsaicin was applied immediately after baseline acquisition of MRS alongside a neutral thermo-pad without removing the participants from the scanner. The thermo-pad was fixed to the skin and covered the area where capsaicin was applied, and was activated by the influx of hot water via plastic tubing conveyed via the penetration panel. A non-heat conducting flexible brace was used to fasten the position of the thermo-pad. The functional MRS followed by acquiring 16 shots every 1.08 min (total = 22.4 min). After 9 min, the thermo-pad was activated by circulating heated water to reach a temperature of approximately 41°C at the forearm. Capsaicin was heat activated for a period of 4.4 min. Functional MRS was acquired continuously during heat application and for the reminder of the scan after the heat was removed. + +Individual FIDs were pre-processed, which included: 0 order phase correction, eddy current correction, frequency alignment, and quality assurance was performed in MATLAB. + +## Acknowledgment + +If using these data, please cite Archibald J., MacMillan EL., Graf C., Kozlowsk P., Laule C., Kramer J.L.K. "Metabolite activity in the anterior cingulate cortex during a painful stimulus using functional MRS". Sci Reports. 10:19218 (2020). doi:10.1038/s41598-020-76263-3. diff --git a/mrs_fmrs/dataset_description.json b/mrs_fmrs/dataset_description.json new file mode 100644 index 000000000..028c564ec --- /dev/null +++ b/mrs_fmrs/dataset_description.json @@ -0,0 +1,21 @@ +{ + "Name": "mrs_fmrs", + "BIDSVersion": "1.10.0", + "DatasetType": "raw", + "License": "CC0 1.0 Universal License", + "Authors": [ + "Jessica Archibald", + "Erin MacMillan", + "John Kramer" + ], + "HowToAcknowledge": "Please cite the following publication if you use the fMRS in pain dataset: Archibald J., MacMillan EL., Graf C., Kozlowski P., Laule C., Kramer J.L.K. 'Metabolite activity in the anterior cingulate cortex during a painful stimulus using functional MRS'. Sci Reports 2020", + "ReferencesAndLinks": [ + "doi:10.1038/s41598-020-76263-3" + ], + "DatasetDOI": "doi:10.25790/bml0cm.159", + "SourceDatasets": [ + { + "URL": "https://www.nitrc.org/projects/fmrs_2020/" + } + ] +} diff --git a/mrs_fmrs/participants.json b/mrs_fmrs/participants.json new file mode 100755 index 000000000..d039ecee0 --- /dev/null +++ b/mrs_fmrs/participants.json @@ -0,0 +1,16 @@ +{ + "participant_id": { + "Description": "Unique participant identifier" + }, + "sex": { + "Description": "Sex of the participant", + "Levels": { + "M": "Male", + "F": "Female" + } + }, + "age": { + "Description": "Age of the participant", + "Units": "years" + } +} diff --git a/mrs_fmrs/participants.tsv b/mrs_fmrs/participants.tsv new file mode 100644 index 000000000..0ee201499 --- /dev/null +++ b/mrs_fmrs/participants.tsv @@ -0,0 +1,16 @@ +participant_id sex age +sub-01 M 35-40 +sub-02 F 25-30 +sub-03 M 20-25 +sub-04 F 25-30 +sub-05 M 25-30 +sub-06 M 30-35 +sub-07 M 25-30 +sub-08 M 20-25 +sub-09 M 25-30 +sub-10 F 20-25 +sub-11 F 20-25 +sub-12 F 20-25 +sub-13 F 25-30 +sub-14 M 25-30 +sub-15 F 20-25 \ No newline at end of file diff --git a/mrs_fmrs/sub-01/anat/sub-01_T1w.json b/mrs_fmrs/sub-01/anat/sub-01_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-01/anat/sub-01_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-01/anat/sub-01_T1w.nii.gz b/mrs_fmrs/sub-01/anat/sub-01_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_mrsref.json b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_mrsref.json new file mode 100644 index 000000000..45fc1b42f --- /dev/null +++ b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-01/anat/sub-01_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_svs.json b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_svs.json new file mode 100644 index 000000000..cdd595782 --- /dev/null +++ b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-01/mrs/sub-01_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-01/anat/sub-01_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_svs.nii.gz b/mrs_fmrs/sub-01/mrs/sub-01_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-pain_events.tsv b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_events.tsv new file mode 100644 index 000000000..cb179b29d --- /dev/null +++ b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 1 +360 120 pre_heat 1 +480 120 pre_heat 1 +600 120 heat 3 +720 120 heat 5 +840 120 post_heat 6 +960 120 post_heat 6 +1080 120 post_heat 7 +1200 120 post_heat 6 \ No newline at end of file diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-pain_mrsref.json b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_mrsref.json new file mode 100644 index 000000000..45fc1b42f --- /dev/null +++ b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-01/anat/sub-01_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-pain_svs.json b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_svs.json new file mode 100644 index 000000000..d6b7c21a9 --- /dev/null +++ b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-01/mrs/sub-01_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-01/anat/sub-01_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-01/mrs/sub-01_task-pain_svs.nii.gz b/mrs_fmrs/sub-01/mrs/sub-01_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-02/anat/sub-02_T1w.json b/mrs_fmrs/sub-02/anat/sub-02_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-02/anat/sub-02_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-02/anat/sub-02_T1w.nii.gz b/mrs_fmrs/sub-02/anat/sub-02_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_mrsref.json b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_mrsref.json new file mode 100644 index 000000000..7221c3455 --- /dev/null +++ b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-02/anat/sub-02_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_svs.json b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_svs.json new file mode 100644 index 000000000..1bf78669a --- /dev/null +++ b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-02/mrs/sub-02_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-02/anat/sub-02_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_svs.nii.gz b/mrs_fmrs/sub-02/mrs/sub-02_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-pain_events.tsv b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_events.tsv new file mode 100644 index 000000000..c34921b4c --- /dev/null +++ b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 1 +480 120 pre_heat 1 +600 120 heat 3 +720 120 heat 5 +840 120 post_heat 4 +960 120 post_heat 1 +1080 120 post_heat 3 +1200 120 post_heat 4 \ No newline at end of file diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-pain_mrsref.json b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_mrsref.json new file mode 100644 index 000000000..7221c3455 --- /dev/null +++ b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-02/anat/sub-02_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-pain_svs.json b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_svs.json new file mode 100644 index 000000000..9892d4600 --- /dev/null +++ b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-02/mrs/sub-02_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-02/anat/sub-02_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-02/mrs/sub-02_task-pain_svs.nii.gz b/mrs_fmrs/sub-02/mrs/sub-02_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-03/anat/sub-03_T1w.json b/mrs_fmrs/sub-03/anat/sub-03_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-03/anat/sub-03_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-03/anat/sub-03_T1w.nii.gz b/mrs_fmrs/sub-03/anat/sub-03_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_mrsref.json b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_mrsref.json new file mode 100644 index 000000000..6979725c8 --- /dev/null +++ b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-03/anat/sub-03_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_svs.json b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_svs.json new file mode 100644 index 000000000..be104b5fe --- /dev/null +++ b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-03/mrs/sub-03_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-03/anat/sub-03_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_svs.nii.gz b/mrs_fmrs/sub-03/mrs/sub-03_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-pain_events.tsv b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_events.tsv new file mode 100644 index 000000000..8a0fb9348 --- /dev/null +++ b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 1 +240 120 pre_heat 1 +360 120 pre_heat 2 +480 120 pre_heat 3 +600 120 heat 5 +720 120 heat 7 +840 120 post_heat 5 +960 120 post_heat 5 +1080 120 post_heat 6 +1200 120 post_heat 7 \ No newline at end of file diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-pain_mrsref.json b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_mrsref.json new file mode 100644 index 000000000..6979725c8 --- /dev/null +++ b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-03/anat/sub-03_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-pain_svs.json b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_svs.json new file mode 100644 index 000000000..ba0e2cdea --- /dev/null +++ b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-03/mrs/sub-03_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-03/anat/sub-03_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-03/mrs/sub-03_task-pain_svs.nii.gz b/mrs_fmrs/sub-03/mrs/sub-03_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-04/anat/sub-04_T1w.json b/mrs_fmrs/sub-04/anat/sub-04_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-04/anat/sub-04_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-04/anat/sub-04_T1w.nii.gz b/mrs_fmrs/sub-04/anat/sub-04_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_mrsref.json b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_mrsref.json new file mode 100644 index 000000000..ee654124c --- /dev/null +++ b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-04/anat/sub-04_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_svs.json b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_svs.json new file mode 100644 index 000000000..ce9b9a0cb --- /dev/null +++ b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-04/mrs/sub-04_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-04/anat/sub-04_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_svs.nii.gz b/mrs_fmrs/sub-04/mrs/sub-04_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-pain_events.tsv b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_events.tsv new file mode 100644 index 000000000..7bd35f70b --- /dev/null +++ b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 1 +360 120 pre_heat 1 +480 120 pre_heat 1 +600 120 heat 3 +720 120 heat 4 +840 120 post_heat 5 +960 120 post_heat 6 +1080 120 post_heat 6 +1200 120 post_heat 6 \ No newline at end of file diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-pain_mrsref.json b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_mrsref.json new file mode 100644 index 000000000..ee654124c --- /dev/null +++ b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-04/anat/sub-04_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-pain_svs.json b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_svs.json new file mode 100644 index 000000000..3fa7d2328 --- /dev/null +++ b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-04/mrs/sub-04_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-04/anat/sub-04_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-04/mrs/sub-04_task-pain_svs.nii.gz b/mrs_fmrs/sub-04/mrs/sub-04_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-05/anat/sub-05_T1w.json b/mrs_fmrs/sub-05/anat/sub-05_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-05/anat/sub-05_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-05/anat/sub-05_T1w.nii.gz b/mrs_fmrs/sub-05/anat/sub-05_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_mrsref.json b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_mrsref.json new file mode 100644 index 000000000..1287bcde7 --- /dev/null +++ b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-05/anat/sub-05_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_svs.json b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_svs.json new file mode 100644 index 000000000..c95cc0475 --- /dev/null +++ b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-05/mrs/sub-05_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-05/anat/sub-05_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_svs.nii.gz b/mrs_fmrs/sub-05/mrs/sub-05_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-pain_events.tsv b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_events.tsv new file mode 100644 index 000000000..6d79ec798 --- /dev/null +++ b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 1 +480 120 pre_heat 1 +600 120 heat 2 +720 120 heat 1 +840 120 post_heat 2 +960 120 post_heat 3 +1080 120 post_heat 4 +1200 120 post_heat 4 \ No newline at end of file diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-pain_mrsref.json b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_mrsref.json new file mode 100644 index 000000000..1287bcde7 --- /dev/null +++ b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-05/anat/sub-05_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-pain_svs.json b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_svs.json new file mode 100644 index 000000000..9062cfcf4 --- /dev/null +++ b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-05/mrs/sub-05_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-05/anat/sub-05_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-05/mrs/sub-05_task-pain_svs.nii.gz b/mrs_fmrs/sub-05/mrs/sub-05_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-06/anat/sub-06_T1w.json b/mrs_fmrs/sub-06/anat/sub-06_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-06/anat/sub-06_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-06/anat/sub-06_T1w.nii.gz b/mrs_fmrs/sub-06/anat/sub-06_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_mrsref.json b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_mrsref.json new file mode 100644 index 000000000..64c218b42 --- /dev/null +++ b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-06/anat/sub-06_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_svs.json b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_svs.json new file mode 100644 index 000000000..ab102f686 --- /dev/null +++ b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-06/mrs/sub-06_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-06/anat/sub-06_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_svs.nii.gz b/mrs_fmrs/sub-06/mrs/sub-06_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-pain_events.tsv b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_events.tsv new file mode 100644 index 000000000..1ab38c526 --- /dev/null +++ b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 1 +600 120 heat 0 +720 120 heat 2 +840 120 post_heat 1 +960 120 post_heat 2 +1080 120 post_heat 2 +1200 120 post_heat 3 \ No newline at end of file diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-pain_mrsref.json b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_mrsref.json new file mode 100644 index 000000000..64c218b42 --- /dev/null +++ b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-06/anat/sub-06_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-pain_svs.json b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_svs.json new file mode 100644 index 000000000..204f7c6bd --- /dev/null +++ b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-06/mrs/sub-06_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-06/anat/sub-06_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-06/mrs/sub-06_task-pain_svs.nii.gz b/mrs_fmrs/sub-06/mrs/sub-06_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-07/anat/sub-07_T1w.json b/mrs_fmrs/sub-07/anat/sub-07_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-07/anat/sub-07_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-07/anat/sub-07_T1w.nii.gz b/mrs_fmrs/sub-07/anat/sub-07_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_mrsref.json b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_mrsref.json new file mode 100644 index 000000000..9d4c9d6c7 --- /dev/null +++ b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-07/anat/sub-07_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_svs.json b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_svs.json new file mode 100644 index 000000000..6fa89b6b3 --- /dev/null +++ b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-07/mrs/sub-07_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-07/anat/sub-07_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_svs.nii.gz b/mrs_fmrs/sub-07/mrs/sub-07_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-pain_events.tsv b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_events.tsv new file mode 100644 index 000000000..73a28fda5 --- /dev/null +++ b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 1 +720 120 heat 5 +840 120 post_heat 3 +960 120 post_heat 3 +1080 120 post_heat 2 +1200 120 post_heat 2 \ No newline at end of file diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-pain_mrsref.json b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_mrsref.json new file mode 100644 index 000000000..9d4c9d6c7 --- /dev/null +++ b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-07/anat/sub-07_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-pain_svs.json b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_svs.json new file mode 100644 index 000000000..9b6dfad3d --- /dev/null +++ b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-07/mrs/sub-07_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-07/anat/sub-07_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-07/mrs/sub-07_task-pain_svs.nii.gz b/mrs_fmrs/sub-07/mrs/sub-07_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-08/anat/sub-08_T1w.json b/mrs_fmrs/sub-08/anat/sub-08_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-08/anat/sub-08_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-08/anat/sub-08_T1w.nii.gz b/mrs_fmrs/sub-08/anat/sub-08_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_mrsref.json b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_mrsref.json new file mode 100644 index 000000000..46c4a151a --- /dev/null +++ b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-08/anat/sub-08_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_svs.json b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_svs.json new file mode 100644 index 000000000..3ab2a2999 --- /dev/null +++ b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-08/mrs/sub-08_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-08/anat/sub-08_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_svs.nii.gz b/mrs_fmrs/sub-08/mrs/sub-08_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-pain_events.tsv b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_events.tsv new file mode 100644 index 000000000..3b809db78 --- /dev/null +++ b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 1 +360 120 pre_heat 1 +480 120 pre_heat 1 +600 120 heat 3 +720 120 heat 6 +840 120 post_heat 4 +960 120 post_heat 2 +1080 120 post_heat 3 +1200 120 post_heat 3 \ No newline at end of file diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-pain_mrsref.json b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_mrsref.json new file mode 100644 index 000000000..46c4a151a --- /dev/null +++ b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-08/anat/sub-08_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-pain_svs.json b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_svs.json new file mode 100644 index 000000000..2817fde39 --- /dev/null +++ b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-08/mrs/sub-08_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-08/anat/sub-08_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-08/mrs/sub-08_task-pain_svs.nii.gz b/mrs_fmrs/sub-08/mrs/sub-08_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-09/anat/sub-09_T1w.json b/mrs_fmrs/sub-09/anat/sub-09_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-09/anat/sub-09_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-09/anat/sub-09_T1w.nii.gz b/mrs_fmrs/sub-09/anat/sub-09_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_mrsref.json b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_mrsref.json new file mode 100644 index 000000000..46db9bff2 --- /dev/null +++ b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-09/anat/sub-09_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_svs.json b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_svs.json new file mode 100644 index 000000000..7c7de0988 --- /dev/null +++ b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-09/mrs/sub-09_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-09/anat/sub-09_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_svs.nii.gz b/mrs_fmrs/sub-09/mrs/sub-09_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-pain_events.tsv b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_events.tsv new file mode 100644 index 000000000..b3dfa5088 --- /dev/null +++ b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 1 +720 120 heat 4 +840 120 post_heat 3 +960 120 post_heat 1 +1080 120 post_heat 2 +1200 120 post_heat 2 \ No newline at end of file diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-pain_mrsref.json b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_mrsref.json new file mode 100644 index 000000000..46db9bff2 --- /dev/null +++ b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-09/anat/sub-09_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-pain_svs.json b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_svs.json new file mode 100644 index 000000000..ca9fc7ae4 --- /dev/null +++ b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-09/mrs/sub-09_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-09/anat/sub-09_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-09/mrs/sub-09_task-pain_svs.nii.gz b/mrs_fmrs/sub-09/mrs/sub-09_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-10/anat/sub-10_T1w.json b/mrs_fmrs/sub-10/anat/sub-10_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-10/anat/sub-10_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-10/anat/sub-10_T1w.nii.gz b/mrs_fmrs/sub-10/anat/sub-10_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_mrsref.json b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_mrsref.json new file mode 100644 index 000000000..704466889 --- /dev/null +++ b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-10/anat/sub-10_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_svs.json b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_svs.json new file mode 100644 index 000000000..bd81369d6 --- /dev/null +++ b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-10/mrs/sub-10_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-10/anat/sub-10_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_svs.nii.gz b/mrs_fmrs/sub-10/mrs/sub-10_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-pain_events.tsv b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_events.tsv new file mode 100644 index 000000000..f9ff90ad3 --- /dev/null +++ b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 2 +240 120 pre_heat 3 +360 120 pre_heat 3 +480 120 pre_heat 6 +600 120 heat 8 +720 120 heat 8 +840 120 post_heat 8 +960 120 post_heat 8 +1080 120 post_heat 8 +1200 120 post_heat 8 \ No newline at end of file diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-pain_mrsref.json b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_mrsref.json new file mode 100644 index 000000000..704466889 --- /dev/null +++ b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-10/anat/sub-10_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-pain_svs.json b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_svs.json new file mode 100644 index 000000000..32aaaee8e --- /dev/null +++ b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-10/mrs/sub-10_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-10/anat/sub-10_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-10/mrs/sub-10_task-pain_svs.nii.gz b/mrs_fmrs/sub-10/mrs/sub-10_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-11/anat/sub-11_T1w.json b/mrs_fmrs/sub-11/anat/sub-11_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-11/anat/sub-11_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-11/anat/sub-11_T1w.nii.gz b/mrs_fmrs/sub-11/anat/sub-11_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_mrsref.json b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_mrsref.json new file mode 100644 index 000000000..5779b459e --- /dev/null +++ b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-11/anat/sub-11_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_svs.json b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_svs.json new file mode 100644 index 000000000..3380b98d0 --- /dev/null +++ b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-11/mrs/sub-11_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-11/anat/sub-11_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_svs.nii.gz b/mrs_fmrs/sub-11/mrs/sub-11_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-pain_events.tsv b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_events.tsv new file mode 100644 index 000000000..c070d9982 --- /dev/null +++ b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 3 +720 120 heat 6 +840 120 post_heat 5 +960 120 post_heat 4 +1080 120 post_heat 4 +1200 120 post_heat 3 \ No newline at end of file diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-pain_mrsref.json b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_mrsref.json new file mode 100644 index 000000000..5779b459e --- /dev/null +++ b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-11/anat/sub-11_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-pain_svs.json b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_svs.json new file mode 100644 index 000000000..cd20ff757 --- /dev/null +++ b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-11/mrs/sub-11_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-11/anat/sub-11_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-11/mrs/sub-11_task-pain_svs.nii.gz b/mrs_fmrs/sub-11/mrs/sub-11_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-12/anat/sub-12_T1w.json b/mrs_fmrs/sub-12/anat/sub-12_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-12/anat/sub-12_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-12/anat/sub-12_T1w.nii.gz b/mrs_fmrs/sub-12/anat/sub-12_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_mrsref.json b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_mrsref.json new file mode 100644 index 000000000..ddf5a0bbc --- /dev/null +++ b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-12/anat/sub-12_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_svs.json b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_svs.json new file mode 100644 index 000000000..8cce06ab0 --- /dev/null +++ b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-12/mrs/sub-12_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-12/anat/sub-12_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_svs.nii.gz b/mrs_fmrs/sub-12/mrs/sub-12_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-pain_events.tsv b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_events.tsv new file mode 100644 index 000000000..03be1f37c --- /dev/null +++ b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 4 +720 120 heat 6 +840 120 post_heat 6 +960 120 post_heat 6 +1080 120 post_heat 5 +1200 120 post_heat 4 \ No newline at end of file diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-pain_mrsref.json b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_mrsref.json new file mode 100644 index 000000000..ddf5a0bbc --- /dev/null +++ b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-12/anat/sub-12_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-pain_svs.json b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_svs.json new file mode 100644 index 000000000..cf9a33098 --- /dev/null +++ b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-12/mrs/sub-12_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-12/anat/sub-12_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-12/mrs/sub-12_task-pain_svs.nii.gz b/mrs_fmrs/sub-12/mrs/sub-12_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-13/anat/sub-13_T1w.json b/mrs_fmrs/sub-13/anat/sub-13_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-13/anat/sub-13_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-13/anat/sub-13_T1w.nii.gz b/mrs_fmrs/sub-13/anat/sub-13_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_mrsref.json b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_mrsref.json new file mode 100644 index 000000000..6c330e0bc --- /dev/null +++ b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-13/anat/sub-13_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_svs.json b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_svs.json new file mode 100644 index 000000000..309419d77 --- /dev/null +++ b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-13/mrs/sub-13_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-13/anat/sub-13_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_svs.nii.gz b/mrs_fmrs/sub-13/mrs/sub-13_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-pain_events.tsv b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_events.tsv new file mode 100644 index 000000000..f5d485fd4 --- /dev/null +++ b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 4 +240 120 pre_heat 5 +360 120 pre_heat 5 +480 120 pre_heat 5 +600 120 heat 7 +720 120 heat 7 +840 120 post_heat 6 +960 120 post_heat 6 +1080 120 post_heat 6 +1200 120 post_heat 5 \ No newline at end of file diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-pain_mrsref.json b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_mrsref.json new file mode 100644 index 000000000..6c330e0bc --- /dev/null +++ b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-13/anat/sub-13_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-pain_svs.json b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_svs.json new file mode 100644 index 000000000..1b47dc398 --- /dev/null +++ b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-13/mrs/sub-13_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-13/anat/sub-13_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-13/mrs/sub-13_task-pain_svs.nii.gz b/mrs_fmrs/sub-13/mrs/sub-13_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-14/anat/sub-14_T1w.json b/mrs_fmrs/sub-14/anat/sub-14_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-14/anat/sub-14_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-14/anat/sub-14_T1w.nii.gz b/mrs_fmrs/sub-14/anat/sub-14_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_mrsref.json b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_mrsref.json new file mode 100644 index 000000000..e5049c964 --- /dev/null +++ b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-14/anat/sub-14_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_svs.json b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_svs.json new file mode 100644 index 000000000..9aa722b05 --- /dev/null +++ b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-14/mrs/sub-14_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-14/anat/sub-14_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_svs.nii.gz b/mrs_fmrs/sub-14/mrs/sub-14_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-pain_events.tsv b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_events.tsv new file mode 100644 index 000000000..d44aba048 --- /dev/null +++ b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 1 +720 120 heat 2 +840 120 post_heat 2 +960 120 post_heat 2 +1080 120 post_heat 3 +1200 120 post_heat 2 \ No newline at end of file diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-pain_mrsref.json b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_mrsref.json new file mode 100644 index 000000000..e5049c964 --- /dev/null +++ b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-14/anat/sub-14_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-pain_svs.json b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_svs.json new file mode 100644 index 000000000..a78f52bad --- /dev/null +++ b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-14/mrs/sub-14_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-14/anat/sub-14_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-14/mrs/sub-14_task-pain_svs.nii.gz b/mrs_fmrs/sub-14/mrs/sub-14_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-15/anat/sub-15_T1w.json b/mrs_fmrs/sub-15/anat/sub-15_T1w.json new file mode 100644 index 000000000..9271a5ee9 --- /dev/null +++ b/mrs_fmrs/sub-15/anat/sub-15_T1w.json @@ -0,0 +1,13 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "MPRAGE", + "MRAcquisitionType": "3D", + "EchoTime": 0.0035, + "InversionTime": 0.808, + "RepetitionTimeExcitation": 0.0077, + "AcquisitionVoxelSize": [1, 1, 1], + "BodyPart": "BRAIN" +} diff --git a/mrs_fmrs/sub-15/anat/sub-15_T1w.nii.gz b/mrs_fmrs/sub-15/anat/sub-15_T1w.nii.gz new file mode 100755 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_mrsref.json b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_mrsref.json new file mode 100644 index 000000000..43d4a606c --- /dev/null +++ b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-15/anat/sub-15_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_mrsref.nii.gz b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_svs.json b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_svs.json new file mode 100644 index 000000000..f59439565 --- /dev/null +++ b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 32, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-15/mrs/sub-15_task-baseline_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-15/anat/sub-15_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_svs.nii.gz b/mrs_fmrs/sub-15/mrs/sub-15_task-baseline_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-pain_events.tsv b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_events.tsv new file mode 100644 index 000000000..56b266045 --- /dev/null +++ b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type pain_rating +120 120 pre_heat 0 +240 120 pre_heat 0 +360 120 pre_heat 0 +480 120 pre_heat 0 +600 120 heat 0 +720 120 heat 2 +840 120 post_heat 3 +960 120 post_heat 5 +1080 120 post_heat 5 +1200 120 post_heat 5 \ No newline at end of file diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-pain_mrsref.json b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_mrsref.json new file mode 100644 index 000000000..43d4a606c --- /dev/null +++ b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_mrsref.json @@ -0,0 +1,21 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": false, + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 16, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "AnatomicalImage": "bids::sub-15/anat/sub-15_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-pain_mrsref.nii.gz b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_mrsref.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-pain_svs.json b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_svs.json new file mode 100644 index 000000000..fcb58f07e --- /dev/null +++ b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_svs.json @@ -0,0 +1,23 @@ +{ + "Manufacturer": "Philips", + "ManufacturersModelName": "Achieva", + "MagneticFieldStrength": 3, + "InstitutionName": "University of British Columbia", + "PulseSequenceType": "PRESS", + "ScanningSequence": "SVS", + "WaterSuppression": true, + "WaterSuppressionTechnique": "Excitation", + "B0ShimmingTechnique": "Second-order", + "BodyPart": "BRAIN", + "BodyPartDetails": "Anterior cingulate cortex", + "ResonantNucleus": ["1H"], + "SpectrometerFrequency": [127.7], + "SpectralWidth": 2000, + "EchoTime": 0.022, + "NumberOfTransients": 320, + "NumberOfSpectralPoints": 2048, + "RepetitionTime": 4, + "AcquisitionVoxelSize": [30, 25, 15], + "ReferenceSignal": "bids::sub-15/mrs/sub-15_task-pain_mrsref.nii.gz", + "AnatomicalImage": "bids::sub-15/anat/sub-15_T1w.nii.gz" +} diff --git a/mrs_fmrs/sub-15/mrs/sub-15_task-pain_svs.nii.gz b/mrs_fmrs/sub-15/mrs/sub-15_task-pain_svs.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tools/print_dataset_listing.py b/tools/print_dataset_listing.py index bfe199c30..9841c2353 100644 --- a/tools/print_dataset_listing.py +++ b/tools/print_dataset_listing.py @@ -9,7 +9,7 @@ import pandas as pd from bids import BIDSLayout -folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site"] +folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site", ".vscode"] suffixes_to_remove = ["README", "description", "participants"] column_order = [ "name", @@ -23,7 +23,7 @@ UPSTREAM_REPO = "https://github.com/bids-standard/bids-examples/tree/master/" # set to True to update the listing of datasets with the datatypes and suffixes -update_content = False +update_content = True root = Path(__file__).resolve().parent.parent input_file = root / "dataset_listing.tsv" @@ -36,6 +36,7 @@ "Microscopy": "micr", "Motion": "motion", "MRI": "func", + "MRS": "mrs", "NIRS": "nirs", "PET": "pet", "qMRI": "", @@ -59,9 +60,12 @@ def main(output_file=None): if update_content: df = update_datatypes_and_suffixes(df, root) df.to_csv(input_file, sep="\t", index=False) + df = pd.read_csv(input_file, sep="\t") df = add_links(df) + print(df) + clean_previous_run(output_file) df = df[column_order] @@ -106,7 +110,7 @@ def update_datatypes_and_suffixes(df, root): def add_links(df): print("Adding hyperlinks in table...") for row in df.iterrows(): - for col in ["name","link to full data", "maintained by"]: + for col in ["name", "link to full data", "maintained by"]: if not isinstance(row[1][col], str): continue if col == "name": @@ -150,6 +154,7 @@ def add_tables(df: pd.DataFrame, output_file: Path) -> None: else: sub_df = df[df["datatypes"].str.contains(table_datatypes, regex=True)] sub_df.sort_values(by=["name"], inplace=True) + # sub_df["name"] = df["name"].apply(lambda x: f'[{x}](https://github.com/bids-standard/bids-examples/tree/master/{x})') print(sub_df) sub_df.to_markdown(output_file, index=False, mode="a") with output_file.open("a") as f: