MED example dataset (no data, only headers) #469

MEDFormat · 2024-10-17T17:42:40Z

relates to bids-standard/bids-specification#1956

Remi-Gau · 2024-10-18T10:55:21Z

@MEDFormat you will have to rename the folders to comply with the BIDS data strcuture.

MEDFormat · 2024-10-18T11:00:49Z

What does that mean? MED & MEF (currently accepted by BIDS) require certain naming conventions. Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 4:55 AM, Remi Gau ***@***.***> wrote: @MEDFormat <https://github.com/MEDFormat> you will have to rename the folders to comply with the BIDS data strcuture. — Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHRSZ6SWWSZ7RBFUJJ3Z4DSLBAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGE4TENBZGQ>. You are receiving this because you were mentioned.

Remi-Gau · 2024-10-18T11:35:47Z

please check any of the other iEEG datasets in this repo and see how the files are named and try top match this.

for example

tree ../examples/ieeg_epilepsy 
../examples/ieeg_epilepsy
├── CHANGES
├── dataset_description.json
├── derivatives
├── participants.json
├── participants.tsv
├── README
└── sub-01
    ├── ses-postimp
    │   ├── anat
    │   │   └── sub-01_ses-postimp_T1w.nii.gz
    │   ├── ieeg
    │   │   ├── sub-01_ses-postimp_space-IXI549Space_coordsystem.json
    │   │   ├── sub-01_ses-postimp_space-IXI549Space_electrodes.tsv
    │   │   ├── sub-01_ses-postimp_space-ScanRAS_coordsystem.json
    │   │   ├── sub-01_ses-postimp_space-ScanRAS_electrodes.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.vhdr
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.vmrk
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.vhdr
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.vmrk
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.vhdr
    │   │   └── sub-01_ses-postimp_task-seizure_run-03_ieeg.vmrk
    │   └── sub-01_ses-postimp_scans.tsv
    └── ses-preimp
        ├── anat
        │   ├── sub-01_ses-preimp_T1w.json
        │   └── sub-01_ses-preimp_T1w.nii.gz
        └── sub-01_ses-preimp_scans.tsv

Given that MED has files listed under a folder I think you may have to follow what is done with MEG for meg.ds

tree ../examples/ds000246 
../examples/ds000246
├── CHANGES
├── dataset_description.json
├── participants.json
├── participants.tsv
├── README
├── sub-0001
│   ├── anat
│   │   └── sub-0001_T1w.nii.gz
│   ├── meg
│   │   ├── sub-0001_acq-LPA_photo.jpg
│   │   ├── sub-0001_acq-NAS_photo.jpg
│   │   ├── sub-0001_acq-RPA_photo.jpg
│   │   ├── sub-0001_coordsystem.json
│   │   ├── sub-0001_headshape.pos
│   │   ├── sub-0001_task-AEF_run-01_channels.tsv
│   │   ├── sub-0001_task-AEF_run-01_meg.ds
│   │   │   ├── BadChannels
│   │   │   ├── ChannelGroupSet.cfg
│   │   │   ├── ClassFile.cls
│   │   │   ├── MarkerFile.mrk
│   │   │   ├── sub-0001_task-AEF_run-01_meg.acq
│   │   │   ├── sub-0001_task-AEF_run-01_meg.eeg
│   │   │   ├── sub-0001_task-AEF_run-01_meg.hc
│   │   │   ├── sub-0001_task-AEF_run-01_meg.hist
│   │   │   ├── sub-0001_task-AEF_run-01_meg.infods
│   │   │   ├── sub-0001_task-AEF_run-01_meg.meg4
│   │   │   └── sub-0001_task-AEF_run-01_meg.res4
│   │   ├── sub-0001_task-AEF_run-01_meg.json
│   │   ├── sub-0001_task-AEF_run-02_channels.tsv
│   │   ├── sub-0001_task-AEF_run-02_meg.ds
│   │   │   ├── BadChannels
│   │   │   ├── ChannelGroupSet.cfg
│   │   │   ├── ClassFile.cls
│   │   │   ├── MarkerFile.mrk
│   │   │   ├── sub-0001_task-AEF_run-02_meg.acq
│   │   │   ├── sub-0001_task-AEF_run-02_meg.eeg
│   │   │   ├── sub-0001_task-AEF_run-02_meg.hc
│   │   │   ├── sub-0001_task-AEF_run-02_meg.hist
│   │   │   ├── sub-0001_task-AEF_run-02_meg.infods
│   │   │   ├── sub-0001_task-AEF_run-02_meg.meg4
│   │   │   ├── sub-0001_task-AEF_run-02_meg.newds
│   │   │   └── sub-0001_task-AEF_run-02_meg.res4
│   │   └── sub-0001_task-AEF_run-02_meg.json
│   └── sub-0001_scans.tsv
└── sub-emptyroom
    ├── meg
    │   ├── sub-emptyroom_task-noise_run-01_channels.tsv
    │   ├── sub-emptyroom_task-noise_run-01_meg.ds
    │   │   ├── BadChannels
    │   │   ├── ClassFile.cls
    │   │   ├── default.de
    │   │   ├── params.dsc
    │   │   ├── processing.cfg
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.acq
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.hc
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.hist
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.infods
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.meg4
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.newds
    │   │   └── sub-emptyroom_task-noise_run-01_meg.res4
    │   └── sub-emptyroom_task-noise_run-01_meg.json
    └── sub-emptyroom_scans.tsv

MEDFormat · 2024-10-18T11:57:44Z

Can you point me to the MEF 3.0 example? I cannot find it, but MED will be almost identical.

MEDFormat · 2024-10-18T12:52:22Z

Contents: Here is a minimal MED tree with all possible file types: Global session records (data & indices) Segmented session records (data & indices) One time series channel (“ts_0001”) One video channel (“vid_0001”) Channel-level records (data & indices) Segment-level records (data & indices) Time series data (data & indices) Time series metadata Video data (data & indices) Video metadata Tree: test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.tidx │ └── ts_0001_s0001.tmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.tidx ├── vid_0001_s0001.tmet └── vid_0001_s0001_n0001.mp4 Descriptions: test.medd: “test” session directory test.medd/test.rdat session record data (unsegmented) test.medd/test..ridx session record indices (unsegmented) test.medd/test.recd: “test” segmented session record directory test.medd/test.recd/test_s0001.rdat segment 1 session record data test.medd/test.recd/test_s0001.ridx segment 1 session record indices test.medd/ts_0001.ticd: “ts_0001” time series channel directory test.medd/ts_0001.rdat: channel-level record data test.medd/ts_0001.ridx: channel-level record indices test.medd/ts_0001_s0001 segment 1 directory test.medd/ts_0001_s0001.tisd/ts_0001_s0001.rdat: segment-level record data test.medd/ts_0001_s0001.tisd/ts_0001_s0001.ridx: segment-level record indices test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tdat: time series data test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tidx: time series indices test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tmet: time series metadata test.medd/vid_0001.vicd: “vid_0001” video channel directory test.medd/vid_0001.rdat: channel-level record data test.medd/vid_0001.ridx: channel-level record indices test.medd/vid_0001_s0001 segment 1 directory test.medd/vid_0001_s0001.tisd/vid_0001_s0001.rdat: segment-level record data test.medd/vid_0001_s0001.tisd/vid_0001_s0001.ridx: segment-level record indices test.medd/vid_0001_s0001.tisd/vid_0001_s0001.vidx: video indices test.medd/vis_0001_s0001.tisd/vid_0001_s0001.vidx: video metadata test.medd/vid_0001_s0001.tisd/vid_0001_s0001_n0001.mp4: video data file 1 (mp4 format in this example) How can I put this information into BIDS example? Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 5:00 AM, Contact MFO ***@***.***> wrote: What does that mean? MED & MEF (currently accepted by BIDS) require certain naming conventions. Cheers, Matt <MFO-Logo-GIF-small.gif> Matt Stead ***@***.*** > On Oct 18, 2024, at 4:55 AM, Remi Gau ***@***.***> wrote: > > > @MEDFormat <https://github.com/MEDFormat> you will have to rename the folders to comply with the BIDS data strcuture. > > — > Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHRSZ6SWWSZ7RBFUJJ3Z4DSLBAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGE4TENBZGQ>. > You are receiving this because you were mentioned. >

MEDFormat · 2024-10-18T12:59:40Z

Copy paste error above:
"vid_0001_s0001.vidx" video metadata
should have been:
"vid_0001_s0001.vmet" video metadata

Remi-Gau · 2024-10-18T13:08:19Z

Can you point me to the MEF 3.0 example?

AFAICT we do not have one

MEDFormat · 2024-10-18T13:12:04Z

Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.vidx │ └── ts_0001_s0001.vmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 7:08 AM, Remi Gau ***@***.***> wrote: Can you point me to the MEF 3.0 example? AFAICT we do not have one — Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHSTF7BWIY5YIZPH2L3Z4EB5VAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGQ2DAMRYGQ>. You are receiving this because you were mentioned.

MEDFormat · 2024-10-18T13:16:13Z

NOTE: made this by hand - last tree had a couple of extension mistakes, apologies. This one is correct. Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.tidx │ └── ts_0001_s0001.tmet └── vid_0001.vicd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.visd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 7:11 AM, Contact MFO ***@***.***> wrote: Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.vidx │ └── ts_0001_s0001.vmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt <MFO-Logo-GIF-small.gif> Matt Stead ***@***.*** > On Oct 18, 2024, at 7:08 AM, Remi Gau ***@***.***> wrote: > > > Can you point me to the MEF 3.0 example? > > AFAICT we do not have one > > — > Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHSTF7BWIY5YIZPH2L3Z4EB5VAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGQ2DAMRYGQ>. > You are receiving this because you were mentioned. >

Remi-Gau · 2024-10-18T13:24:57Z

I think your dataset should be structured like this

├── dataset_description.json
├── README.md
└── sub-01
    └── sub-01_task-TaskName_ieeg.medd

where sub-01_task-TaskName_ieeg.medd is actually the test.medd from above.

Remi-Gau · 2024-10-18T13:27:19Z

but you are going to require some extra json files

see https://bids-specification.readthedocs.io/en/stable/modality-specific-files/intracranial-electroencephalography.html#sidecar-json-_ieegjson

effigies · 2024-10-18T13:37:10Z

@MEDFormat @Remi-Gau I've copied a pared down version of ieeg_epilepsy and replaced the _ieeg.* files with an _ieeg.medd directory and pushed to this PR.

Making some additional changes to adjust validator behavior, given that we aren't targeting the legacy validator and the schema changes havn't been merged yet.

Add files via upload

adc75fa

effigies added 4 commits October 18, 2024 09:29

Attempt to update test.medd to broadly follow ieeg_epilepsy

0771b30

Update scans.tsv

0087b85

Skip legacy validation

893fc5a

Import schema from branch that introduces MED format

969bb2d

Typo in scans.tsv

abd0ea5

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MED example dataset (no data, only headers) #469

MED example dataset (no data, only headers) #469

MEDFormat commented Oct 17, 2024 •

edited by Remi-Gau

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effigies commented Oct 18, 2024

MED example dataset (no data, only headers) #469

Are you sure you want to change the base?

MED example dataset (no data, only headers) #469

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