Hi fmriprep fans… can you help me understand what this crash report is saying?
I am running fmriprep (v20.2.3) and running into an error. I post the crash report below.
I don’t seem to be having this issue on other data so I am guessing that this may be something specific about this dataset but I can not for the life of me see what the problem is!
Would anyone be able to help me out understanding what happened here based on the crash report below?
I ran the command:
fmriprep \
${source_data} \
${output_data} \
participant \
--participant_label ${subject} \
--task-id rest \
--bold2t1w-dof 12 \
--work-dir ${work} \
--write-graph \
--nthreads 2 \
--omp-nthreads 2 \
--dummy-scans 10 \
--use-aroma \
--use-syn-sdc \
--fs-license-file ${working_dir}/license.txt \
-vv \
--error-on-aroma-warnings \
--stop-on-first-crash
…and get:
Crash Report:
Node: _t1w_conform_xfm0
Working directory: /1_fMRIprep/work/sub-F002/fmriprep_wf/single_subject_F002_wf/anat_preproc_wf/anat_template_wf/t1w_conform_xfm/mapflow/_t1w_conform_xfm0
Node inputs:
args = <undefined>
environ = {}
in_fsl = <undefined>
in_itk = <undefined>
in_lta = identity.nofile
in_mni = <undefined>
in_niftyreg = <undefined>
in_reg = <undefined>
invert = <undefined>
ltavox2vox = <undefined>
out_fsl = <undefined>
out_itk = <undefined>
out_lta = True
out_mni = <undefined>
out_reg = <undefined>
source_file = /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz
target_conform = <undefined>
target_file = /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 753, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
lta_convert --inlta identity.nofile --outlta /1_fMRIprep/work/sub-F002/fmriprep_wf/single_subject_F002_wf/anat_preproc_wf/anat_template_wf/t1w_conform_xfm/mapflow/_t1w_conform_xfm0/out.lta --src /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz --trg /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz
Standard output:
$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $
--inlta: identity.nofile input LTA transform.
--outlta: /1_fMRIprep/work/sub-F002/fmriprep_wf/single_subject_F002_wf/anat_preproc_wf/anat_template_wf/t1w_conform_xfm/mapflow/_t1w_conform_xfm0/out.lta output LTA.
--src: /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz src image (geometry).
--trg: /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz trg image (geometry).
ERROR: could not determine type of /1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz
Standard error:
ERROR readLTA: cannot read src MRI/1_fMRIprep/bids_data/sourcedata/sub-F002/ses-V2/anat/sub-F002_ses-V2_T1w.nii.gz
Return code: 1