Hi,
Summary of what happened:
I am running qsiprep to preprocess dwi files with phase diff fmaps and t1
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B ${WORK_DIR}:/work \
-B $OUTPUT:/out \
-B $BIDSROOT:/data \
${CONTAINER_DIR}/qsiprep-0.21.4.sif \
/data /out participant \
--participant-label $SUBJECT_NUM \
-w /work \
--skip-bids-validation \
--verbose \
--fs-license-file $FS_LICENSE \
--stop-on-first-crash \
--output-resolution 2 \
--unringing-method mrdegibbs --denoise-method dwidenoise \
--hmc_model eddy \
Version:
0.21.4
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity / Apptainer
it’s already installed on the computing machine and I am loading it with:
module load StdEnv/2023 apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
yes it is BIDS format
Relevant log outputs (up to 20 lines):
240619-05:26:18,555 nipype.workflow IMPORTANT:
Creating dwi processing workflow "dwi_preproc_ses_01_wf" to produce output sub-001_ses-01 (1.06 GB / 82 DWIs). Memory resampled/largemem=1.23/1.29 GB.
240619-05:26:18,557 nipype.workflow INFO:
Automatically using 5, 5, 5 window for dwidenoise
240619-05:26:21,24 nipype.workflow INFO:
Using 8 threads in eddy
240619-05:26:21,40 nipype.workflow INFO:
Computing fieldmap directly from phasediff
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 1091, in build_qsiprep_workflow
retval["workflow"] = init_qsiprep_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 237, in init_qsiprep_wf
single_subject_wf = init_single_subject_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 748, in init_single_subject_wf
dwi_preproc_wf = init_dwi_preproc_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/base.py", line 406, in init_dwi_preproc_wf
hmc_wf = init_fsl_hmc_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/fsl.py", line 422, in init_fsl_hmc_wf
b0_sdc_wf = init_sdc_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/fieldmap/base.py", line 244, in init_sdc_wf
sdc_unwarp_wf = init_sdc_unwarp_wf(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/fieldmap/unwarp.py", line 180, in init_sdc_unwarp_wf
vsm2dfm = pe.Node(itk.FUGUEvsm2ANTSwarp(), name="vsm2dfm")
AttributeError: module 'niworkflows.interfaces.itk' has no attribute 'FUGUEvsm2ANTSwarp'