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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
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*
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
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
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 themrtrix_multishell_msmt_ACT-hsvs
workflow should be written to thebids/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 frombids/derivatives/qsirecon/<participant_id>/<session_id>/dwi/
.Reproducing the bug
Retrieving the atlases from AtlasPack and resampling to the LPS template from QSIPrep:
Download QSIPrep's MNI152NLin2009cAsym standard (mni_1mm_t1w_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.jsonSingularity run command from slurm script:
Slurm Terminal Output is attached here
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