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[RF] Remove the recon workflows from QSIPrep #802

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merged 36 commits into from
Aug 14, 2024
Merged

[RF] Remove the recon workflows from QSIPrep #802

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6778bfa
remove recon workflows
mattcieslak Aug 9, 2024
2e59c7d
more deletions
mattcieslak Aug 9, 2024
01c4c95
remove references to recon
mattcieslak Aug 9, 2024
f8f08c7
continued
mattcieslak Aug 10, 2024
5f55fa1
reports
mattcieslak Aug 11, 2024
ce8030e
Send logs to output directory
mattcieslak Aug 12, 2024
3994b68
lint + output_dir
mattcieslak Aug 12, 2024
1e2710b
again
mattcieslak Aug 12, 2024
52871e7
Works locally
mattcieslak Aug 12, 2024
e4f6ea5
Fix up tests.
tsalo Aug 12, 2024
497df16
qsiprep_dir --> output_dir
tsalo Aug 12, 2024
e0b70c4
No out_base_path.
tsalo Aug 12, 2024
f3dca65
Update test_cli.py
tsalo Aug 12, 2024
7a4d7c3
Update.
tsalo Aug 12, 2024
81df080
Update base.py
tsalo Aug 12, 2024
2a41ba4
Update reports.py
tsalo Aug 12, 2024
b70a936
Remove exec_mode.
tsalo Aug 12, 2024
fe87acb
Remove pipeline_type.
tsalo Aug 12, 2024
0f31178
Replace DerivativesDataSink.
tsalo Aug 13, 2024
cbe7efc
Run isort.
tsalo Aug 13, 2024
5b03678
Update io_spec.json
tsalo Aug 13, 2024
edcac1a
Update io_spec.json
tsalo Aug 13, 2024
0df23c9
Fix.
tsalo Aug 13, 2024
4264dd0
Update expected outputs.
tsalo Aug 13, 2024
982a55c
Fix stuff.
tsalo Aug 13, 2024
90e3a44
Update merge.py
tsalo Aug 13, 2024
471025a
Update io_spec.json
tsalo Aug 13, 2024
8f472df
Drop reportlets_dir.
tsalo Aug 13, 2024
c3fa764
Update.
tsalo Aug 13, 2024
b78153d
Generalize fix_multi_source_name.
tsalo Aug 13, 2024
39d32fd
Update misc.py
tsalo Aug 13, 2024
184ad86
Update misc.py
tsalo Aug 13, 2024
fa01fc4
Update misc.py
tsalo Aug 13, 2024
6304007
Fix up tests.
tsalo Aug 14, 2024
b0360ec
Update expected outputs.
tsalo Aug 14, 2024
302f030
Update expected outputs.
tsalo Aug 14, 2024
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47 changes: 0 additions & 47 deletions .circleci/3TissueAutotrackTest.sh
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65 changes: 0 additions & 65 deletions .circleci/3TissueReconTests.sh
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48 changes: 0 additions & 48 deletions .circleci/AMICOReconTests.sh
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3 changes: 1 addition & 2 deletions .circleci/AllFieldmaps.sh
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Expand Up @@ -5,14 +5,13 @@ cat << DOC
AllFieldmaps test
=================

Instead of running full workflows, this test checks that workflows can
Instead of running full workflows, this test checks that workflows can
be built for all sorts of fieldmap configurations.

This tests the following features:
- Blip-up + Blip-down DWI series for TOPUP/Eddy
- Eddy is run on a CPU
- Denoising is skipped
- A follow-up reconstruction using the dsi_studio_gqi workflow

Inputs:
-------
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43 changes: 0 additions & 43 deletions .circleci/AutoTrackTest.sh
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62 changes: 0 additions & 62 deletions .circleci/DIPYReconTests.sh
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4 changes: 1 addition & 3 deletions .circleci/DSDTI_TOPUP.sh
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Expand Up @@ -9,7 +9,6 @@ This tests the following features:
- TOPUP on a single-shell sequence
- Eddy is run on a CPU
- mrdegibbs is run
- A follow-up reconstruction using the dsi_studio_gqi workflow

Inputs:
-------
Expand All @@ -23,7 +22,7 @@ source ./get_data.sh
TESTDIR=${PWD}
TESTNAME=DSDTI_TOPUP
get_config_data ${TESTDIR}
get_bids_data ${TESTDIR} DSDTI
#get_bids_data ${TESTDIR} DSDTI
CFG=${TESTDIR}/data/nipype.cfg
EDDY_CFG=${TESTDIR}/data/eddy_config.json

Expand All @@ -41,7 +40,6 @@ ${QSIPREP_CMD} \
--sloppy \
--unringing-method mrdegibbs \
--b1-biascorrect-stage legacy \
--recon-spec dsi_studio_gqi \
--eddy_config ${EDDY_CFG} \
--output-resolution 5 \
-vv
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1 change: 0 additions & 1 deletion .circleci/DSDTI_nofmap.sh
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Expand Up @@ -9,7 +9,6 @@ This tests the following features:
- A workflow with no distortion correction followed by eddy
- Eddy is run on a CPU
- Denoising is skipped
- A follow-up reconstruction using the dsi_studio_gqi workflow

Inputs:
-------
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68 changes: 0 additions & 68 deletions .circleci/DSDTI_outputs.txt
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Expand Up @@ -46,72 +46,4 @@ qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_sampling_scheme.gif
qsiprep/sub-PNC/figures/sub-PNC_seg_brainmask.svg
qsiprep/sub-PNC/figures/sub-PNC_t1_2_mni.svg
qsiprep/sub-PNC.html
qsirecon
qsirecon/dwiqc.json
qsirecon/logs
qsirecon/logs/CITATION.html
qsirecon/logs/CITATION.md
qsirecon/logs/CITATION.tex
qsirecon/sub-PNC
qsirecon/sub-PNC/dwi
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-ad_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-dti_fa_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa0_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa1_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa2_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gfa_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-iso_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-md_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-rd_gqiscalar.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_atlas.mif.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_atlas.nii.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_mrtrixLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_origLUT.txt
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_gqi.fib.gz
qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_gqinetwork.mat
qsirecon/sub-PNC/figures
qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-DSIStudioConnectivity_matrices.svg
qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-GQIODF_odfs.png
qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-GQIODF_peaks.png
qsirecon/sub-PNC.html
/tmp/DSDTI/derivatives
1 change: 0 additions & 1 deletion .circleci/DSDTI_synfmap.sh
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Expand Up @@ -9,7 +9,6 @@ This tests the following features:
- A workflow with no distortion correction followed by eddy
- Eddy is run on a CPU
- Denoising is skipped
- A follow-up reconstruction using the dsi_studio_gqi workflow

Inputs:
-------
Expand Down
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