Hi - have been scouring the internet to try to understand why my fmriprep is failing at autocon when running through singularity on a supercomputer.
What happened?
Autorecon 1 appears to be failing and not providing a helpful error message.
My code running on a Super Computer
singularity run --cleanenv /work/06953/jes6785/Containers/fmriprep_latest.sif /scratch/06953/jes6785/Pre_Process_Test/ /scratch/06953/jes6785/fmri_prep/ participant --participant-label b005 --fs-license-file /scratch/06953/jes6785/NECTARY_DATA/code/license.txt --skip_bids_validation -w /scratch/06953/jes6785/working_dir/
I have tried this discussion Autorecon1 Crashing · Issue #286 · nipreps/smriprep · GitHub
but the only thing that I have in my ```
/fmriprep_22_0_wf/single_subject__wf/anat_preproc_wf/surface_recon_wf/autorecon1/command.txt is a note that says
“echo reconall-all: nothing to do”
###Here is my error script…
Node: _parcstats1
Working directory: /scratch/06953/jes6785/working_dir/fmriprep_22_0_wf/single_subject_b005_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1
Node inputs:
FLAIR_file =
T1_files =
T2_file =
args =
big_ventricles =
brainstem =
directive = autorecon-hemi
environ = {}
expert =
flags = [’-nohyporelabel’]
hemi = rh
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires =
mprage =
mri_aparc2aseg =
mri_ca_label =
mri_ca_normalize =
mri_ca_register =
mri_edit_wm_with_aseg =
mri_em_register =
mri_fill =
mri_mask =
mri_normalize =
mri_pretess =
mri_remove_neck =
mri_segment =
mri_segstats =
mri_tessellate =
mri_watershed =
mris_anatomical_stats =
mris_ca_label =
mris_fix_topology =
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 8
parallel =
steps =
subject_id = sub-b005
subjects_dir = /scratch/06953/jes6785/fmri_prep/sourcedata/freesurfer
talairach =
use_FLAIR =
use_T2 =
xopts =
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 _parcstats1.
RuntimeError: subprocess exited with code 1.