Summary of what happened:
I’m trying to preprocess some data with qsiprep and there seem to be some issues with the .hmc_sdc_wf.sdc_wf.sdc_unwarp_wf.fmap2ref_apply step, specifically the call to antsApplyTransforms where the dimensionality (3) does not match the dimensions of the reference image (4). The field maps we are using are case 3. I’m not sure if there’s some flag I should set during my call to qsiprep that I’m missing or if there’s something else going on. Any advice is most welcome!
Command used (and if a helper script was used, a link to the helper script or the command generated):
`
singularity run --cleanenv /<path_to_image>/qsiprep_unstable.sif \
/<path-to-input> \
/<path-to-input>/derivatives participant --participant-label sub-<participant_id> \
--prefer_dedicated_fmaps \
-w /path/to/work \
--output-resolution 1.5
Version:
qsiprep version: 0.17.0
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Data formatted according to BIDS standard
Relevant log outputs (up to 20 lines):
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node fmap2ref_apply.
Cmdline:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1
--input /<work_dir>/hmc_sdc_wf/sdc_wf/fmap_wf/applymsk/<subject_id>_acq-60_fieldmap_ras_rad_unwrapped_hz_filt_demean_maths_masked.nii.gz
--interpolation BSpline
--output <subject_id>_acq-60_fieldmap_ras_rad_unwrapped_hz_filt_demean_maths_masked_trans.nii.gz
--reference-image <work_dir>/dwi_preproc_acq_60_wf/hmc_sdc_wf/b0_ref_to_lps/topup_imain_LPS.nii.gz
--transform <work_dir>/dwi_preproc_acq_60_wf/hmc_sdc_wf/sdc_wf/sdc_unwarp_wf/fmap2ref_reg/transformComposite.h5
Stdout:
Stderr:
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 399, in run
runtime = self._post_run_hook(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/niworkflows/interfaces/registration.py", line 106, in _post_run_hook
return super(ANTSApplyTransformsRPT, self)._post_run_hook(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/mixins/reporting.py", line 50, in _post_run_hook
self._generate_report()
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/niworkflows/interfaces/report_base.py", line 61, in _generate_report
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/niworkflows/viz/utils.py", line 215, in cuts_from_bbox
ras_coords.append(apply_affine(mask_nii.affine, cross).tolist())
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/affines.py", line 97, in apply_affine
pts = pts @ rzs.T + trans[None, :]
ValueError: matmul: Input operand 1 has a mismatch in its core dimension 0, with gufunc signature (n?,k),(k,m?)->(n?,m?) (size 3 is different from 4)