fmriprep: Error for single subject

Hi, I had run the workflow for a single subject but ran into the following error. The command I had used was: sudo fmriprep-docker --fs-license-file /some_dir/Freesurfer_license/license.txt /some_dir/LMU_BIDS_3 /some_dir/LMU_3_processed participant --participant_label sub-0025402

Error on “fmriprep_wf.single_subject_0025402_wf.anat_preproc_wf.anat_template_wf.t1_merge” (/root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/t1_merge) Traceback (most recent call last): File “/usr/local/miniconda/bin/fmriprep”, line 11, in <module> sys.exit(main()) File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 316, in main fmriprep_wf.run(**plugin_settings) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py”, line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 162, in run self._clean_queue(jobid, graph, result=result)) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 224, in _clean_queue raise RuntimeError(“”.join(result[‘traceback’])) RuntimeError: Traceback (most recent call last): File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node result[‘result’] = node.run(updatehash=updatehash) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 480, in run result = self._run_interface(execute=True) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface return self._run_command(execute) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 644, in _run_command result = self._interface.run(cwd=outdir) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py”, line 275, in run return super(FSCommandOpenMP, self).run(**inputs) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py”, line 144, in run return super(FSCommand, self).run(**inputs) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 521, in run runtime = self._run_interface(runtime) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 1033, in _run_interface self.raise_exception(runtime) File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 970, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: mri_robust_template --satit --fixtp --mov /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-0025402_ses-01_T1w_ras_corrected.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-0025402_ses-02_T1w_ras_corrected.nii.gz --inittp 1 --iscale --noit --template sub-0025402_ses-01_T1w_ras_template.nii.gz --subsample 200 --lta /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

–satit: Will estimate SAT iteratively! –fixtp: Will map everything to init TP! –mov: Using /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-0025402_ses-01_T1w_ras_corrected.nii.gz as movable/source volume. –mov: Using /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-0025402_ses-02_T1w_ras_corrected.nii.gz as movable/source volume. Total: 2 input volumes –inittp: Using TP 1 as target for initialization –iscale: Enableing intensity scaling! –noit: Will output only first template (no iterations)! –template: Using sub-0025402_ses-01_T1w_ras_template.nii.gz as template output volume. –subsample: Will subsample if size is larger than 200 on all axes! –lta: Will output LTA transforms Setting iscale … reading source ‘/root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-0025402_ses-01_T1w_ras_corrected.nii.gz’… converting source ‘/root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-0025402_ses-01_T1w_ras_corrected.nii.gz’ to bspline … MRItoBSpline degree 3 reading source ‘/root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-0025402_ses-02_T1w_ras_corrected.nii.gz’… converting source ‘/root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-0025402_ses-02_T1w_ras_corrected.nii.gz’ to bspline … MRItoBSpline degree 3

MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :

[init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-0025402_ses-02_T1w_ras_corrected.nii.gz ) to TP 1 ( /root/src/fmriprep/work/fmriprep_wf/single_subject_0025402_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-0025402_ses-01_T1w_ras_corrected.nii.gz )

Standard error: Killed Return code: 137

Sentry is attempting to send 1 pending error messages Waiting up to 10 seconds Press Ctrl-C to quit fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues