Summary of what happened:
Hello!
I have run fMRIprep (v. 22.0.1) once on my data (just one subject, one session, two runs). When I first ran it, I used my fMRIprep command to run recon-all. Now, I want to run it again, but this time I would like to use the recon-all outputs that I got from my first time running fMRIprep (they are stored in bids-root/derivatives/sourcedata/freesurfer, and are in a BIDS compatible format). Unfortunately, it crashed, and I am not sure how to address the issue.
I’m confused as to why everything was undefined, and also confused how my subject ID got set to “recon_all” …?
Is there any way to fix this? I am running fMRIprep on an institutional HPC and the only fMRIprep versions that we have installed on it are v22.0.1 and v20.2.3.
Thanks!
Ryann
Command used (and if a helper script was used, a link to the helper script or the command generated):
FMRIPREP=/global/software/fmriprep/containers/fmriprep-22.0.1.simg
singularity run $FMRIPREP bids-root bids-root/derivatives3 participant \
--fs-license-file license.txt \
--fs-subjects-dir bids-root/derivatives/sourcedata/freesurfer \
-w fmriprep_work_dir3
Version:
22.0.1
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Node: fmriprep_22_0_wf.single_subject_AUDXX1_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Working directory: /home/ryann.tansey/fmriprep_work_dir3/fmriprep_22_0_wf/single_subject_AUDXX1_wf/anat_preproc_wf/surface_recon_wf/autorecon1
Node inputs:
FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon1
environ = {}
expert = <undefined>
flags = <undefined>
hemi = <undefined>
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
steps = <undefined>
subject_id = recon_all
subjects_dir = <undefined>
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1.
RuntimeError: subprocess exited with code 1.