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Hello,
I am running some freesurfer processes
(freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275) via fmriprep
23.1.3 (singularity container version) and I'm getting the error below when
running the mris_expand command. Below is the output from frmiprep but it's
clear it's a freesurfer-specific error (I've highlighted the freesurfer
command, output, and error in red). There was another post with the buffer
overflow detected error (different command though) and it did not have a
posted solution.
Node: _midthickness0
Working directory:
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0
Node inputs:
args = <undefined>
distance = 0.5
dt = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'}
graymid = <undefined>
in_file =
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/temp/_epo/derivatives/fmriprep23_1_3/sourcedata/freesurfer/sub-10412/surf/rh.white
nsurfaces = <undefined>
out_name = midthickness
pial = <undefined>
smooth_averages = <undefined>
sphere = sphere
spring = <undefined>
subjects_dir = /opt/freesurfer/subjects
thickness = True
thickness_name = <undefined>
write_iterations = <undefined>
Traceback (most recent call last):
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py",
line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py",
line 527, in run
result = self._run_interface(execute=True)
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py",
line 645, in _run_interface
return self._run_command(execute)
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py",
line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while
executing Node _midthickness0.
Cmdline:
mris_expand -pial
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial
-thickness -thickness_name
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white
0.5
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness
Stdout:
reading pial surface from
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial
using distance as a % of thickness
using thickness file
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness
expanding surface
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white
by 50.0% of thickness and writing it to
/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness
reading thickness...
Stderr:
*** buffer overflow detected ***: terminated
Aborted (core dumped)
Traceback:
RuntimeError: subprocess exited with code 134.
--
Amanda Rodrigue, PhD
Boston Children's Hospital
Harvard Medical School
1 Autumn St.
Boston, MA 02215
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