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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.