fmriprep/freesurfer can't open rh.cortex.label even though it exists

[jbwexler]

I'm pretty sure this issue is being caused by the fact that I was accidentally copying links instead of the actual file when replacing missing fsaverage and fsaverage5 files. I'm testing now to see if this was the issue.

Here's the full output of an example crash file:

(main) login4.frontera(1018)$ cat /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds000117-fmriprep/sub-01/log/20220228-075311_fca40b24-c8f5-4e61-b877-cd051e4819d8/crash-20220228-091805-jbwexler-_sampler1-a2a7419f-2818-4d76-8b5d-7dc5640981f3.txt Node: _sampler1 Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/_target_fsaverage/sampler/mapflow/_sampler1

Node inputs:

apply_rot = apply_trans = args = cortex_mask = True environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} fix_tk_reg = float2int_method = frame = hemi = rh hits_file = hits_type = ico_order = interp_method = trilinear mask_label = mni152reg = no_reshape = out_file = out_type = gii override_reg_subj = True projection_stem = reference_file = reg_file = /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/itk2lta/out.lta reg_header = reshape = reshape_slices = sampling_method = average sampling_range = (0.0, 1.0, 0.2) sampling_units = frac scale_input = smooth_surf = smooth_vol = source_file = /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/_target_fsaverage/rename_src/fsaverage.nii subject_id = sub-01 subjects_dir = /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds000117-fmriprep/sourcedata/freesurfer surf_reg = surface = target_subject = fsaverage vox_file =

Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/base.py", line 149, in run return super(FSCommand, self).run(**inputs) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception raise RuntimeError( RuntimeError: Command: mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/_target_fsaverage/sampler/mapflow/_sampler1/rh.fsaverage.gii --srcsubject sub-01 --reg /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/itk2lta/out.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/_target_fsaverage/rename_src/fsaverage.nii --trgsubject fsaverage Standard output: srcvol = /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/_target_fsaverage/rename_src/fsaverage.nii srcreg = /scratch1/03201/jbwexler/work_dir/fmriprep/ds000117_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_ses_mri_task_facerecognition_run_09_wf/bold_surf_wf/itk2lta/out.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm Done loading volume INFO: overriding regsubject with sub-01 Input reg is LTA -------- original matrix ----------- -1.00000 0.00042 0.00036 -0.11612; 0.00036 0.00031 1.00000 11.82422; -0.00042 -1.00000 0.00031 -17.68887; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds000117-fmriprep/sourcedata/freesurfer/fsaverage/label/rh.cortex.label Standard error: No such file or directory mri_vol2surf: could not open label file /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds000117-fmriprep/sourcedata/freesurfer/fsaverage/label/rh.cortex.label Invalid argument mri_vol2surf: could not load label file /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds000117-fmriprep/sourcedata/freesurfer/fsaverage/label/rh.cortex.label Invalid argument Return code: 255

[effigies]

Probably need to datalad get...

[jbwexler]

They actually weren't annexed but were linked to files on corral. Kind of a long story how they ended up that way.