Reconstruction dwi outputs not included in derivatives when using a custom atlas

[pcamach2]

Summary

A custom reconstruction workflow using a custom atlas seems to complete according to the working directory outputs, but the output is not written to the derivatives folder.

Additional details

• QSIPrep version: v0.19.1
• Docker version: N/A
• Singularity version: singularity-ce version 3.10.5-1.el7

This was originally discussed on NeuroStars Qsiprep custom atlas does not output connectivity matrices. @mattcieslak suggested that there could be an issue with the derivatives datasink.

This could also perhaps be something to update in adding subcortical regions in https://github.com/PennLINC/qsiprep-atlas/blob/7f70b79c531052d0e68e2e5528537e37033f5e12/QSIRecon%20atlases.ipynb

What were you trying to do?

Using a custom atlas parcellation - specifically the AtlasPack 4S156 and 4S256 atlases - as described here for the

What did you expect to happen?

The custom atlas connectivity matrix .mat files and other associated outputs of the mrtrix_multishell_msmt_ACT-hsvs workflow should be written to the bids/derivatives/qsirecon/<participant_id>/<session_id>/dwi/ folder.

What actually happened?

Only the anatomical outputs, figures, and HTML report are generated in bids/derivatives/qsirecon/. The working directory qsirecon_wf folders contain the <atlas>_<edge_weight>_connectivity.mat files, the exemplar .tck files, and the other pieces that I would expect from this reconstruction pipeline. However, the corresponding outputs are missing from bids/derivatives/qsirecon/<participant_id>/<session_id>/dwi/.

$ ls bids/derivatives/qsirecon/sub-PROJECT176/*
bids/derivatives/qsirecon/sub-PROJECT176/anat:
sub-PROJECT176_desc-preproc_desc-hsvs_5tt.nii.gz  sub-PROJECT176_desc-preproc_space-fsnative_desc-hsvs_5tt.mif

bids/derivatives/qsirecon/sub-PROJECT176/figures:
sub-PROJECT176_ses-A_run-1_space-T1w_desc-preproc_desc-MRtrix3Connectivity_matrices.svg  sub-PROJECT176_ses-A_run-1_space-T1w_desc-preproc_desc-wmFOD_peaks.png
sub-PROJECT176_ses-A_run-1_space-T1w_desc-preproc_desc-wmFOD_odfs.png

Reproducing the bug

Retrieving the atlases from AtlasPack and resampling to the LPS template from QSIPrep:

datalad clone https://github.com/PennLINC/AtlasPack.git​
datalad get tpl*MNI*4S156* && datalad get tpl*MNI*4S256*​

Download QSIPrep's MNI152NLin2009cAsym standard (mni_1mm_t1w_lps.nii.gz)​

3dresample -input tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg.nii.gz -master ~/Downloads/mni_1mm_t1w_lps.nii.gz -prefix tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg_lps.nii.gz​

3dresample -input tpl-MNI152NLin2009cAsym_atlas-4S256Parcels_res-01_dseg.nii.gz -master ~/Downloads/mni_1mm_t1w_lps.nii.gz -prefix tpl-MNI152NLin2009cAsym_atlas-4S256Parcels_res-01_dseg_lps.nii.gz​

Adapt atlas_config.json (using parcel labels from XCP-D conmat.tsv to generate labels for each atlas​) and reconstruction pipeline JSON (add to atlas_config.json under new entries​). See attached files atlas_config.json and mrtrix_multishell_msmt_ACT-hsvs_4S.json

Singularity run command from slurm script:

SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv \
--bind ${IMAGEDIR}:/imgdir,${IMAGEDIR}/4S/mrtrix_multishell_msmt_ACT-hsvs_4S.json:/atlas/qsirecon_atlases/mrtrix_multishell_msmt_ACT-hsvs_4S.json \
--bind ${IMAGEDIR}/4S/atlas_config.json:/atlas/qsirecon_atlases/atlas_config.json \
--bind ${IMAGEDIR}/4S/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg_lps.nii.gz:/atlas/qsirecon_atlases/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg.nii.gz \
--bind ${IMAGEDIR}/4S/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg_lps.nii.gz:/atlas/qsirecon_atlases/tpl-MNI152NLin2009cAsym_atlas-4S256Parcels_res-01_dseg.nii.gz \
--bind ${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.19.1.sif --fs-license-file /imgdir/license.txt \
/data/bids/sourcedata /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep \
--freesurfer-input /data/bids/derivatives/fmriprep/freesurfer \
--recon_spec /atlas/qsirecon_atlases/mrtrix_multishell_msmt_ACT-hsvs_4S.json \
--output-resolution 2.5 -w /paulscratch participant --participant-label ${subject}

Slurm Terminal Output is attached here