Node: fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1 Working directory: /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1 Node inputs: FLAIR_file = T1_files = ['/data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] T2_file = args = big_ventricles = brainstem = directive = autorecon1 environ = {} expert = flags = ['-noskullstrip'] hemi = hippocampal_subfields_T1 = hippocampal_subfields_T2 = hires = True 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 = -n 50 mris_make_surfaces = mris_register = mris_smooth = mris_sphere = mris_surf2vol = mrisp_paint = openmp = 8 parallel = steps = subject_id = sub-01 subjects_dir = /out/sourcedata/freesurfer talairach = use_FLAIR = use_T2 = xopts = 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/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: recon-all -autorecon1 -noskullstrip -hires -openmp 8 -subjid sub-01 -sd /out/sourcedata/freesurfer -xopts-use -nomotioncor -notalairach -nonuintensitycor Standard output: INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/sourcedata/freesurfer Actual FREESURFER_HOME /opt/freesurfer -rwxr-xr-x 1 root root 52120 Jul 19 17:04 /out/sourcedata/freesurfer/sub-01/scripts/recon-all.log Linux adaf922e9c1a 4.9.13-moby #1 SMP Tue Mar 21 21:21:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/sourcedata/freesurfer/sub-01/scripts/recon-all.local-copy' #-------------------------------------------- #@# Intensity Normalization Tue Jul 19 17:34:53 UTC 2022 /out/sourcedata/freesurfer/sub-01/mri mri_normalize -g 1 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform 0.70656 -0.02942 0.04308 7.65156; 0.03499 0.70119 -0.09508 -60.39386; -0.03869 0.09695 0.70075 174.74060; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks. Make sure the Talairach alignment is correct! MRInormalize(): 1d normalization failed - trying no1d... Segmentation fault Linux adaf922e9c1a 4.9.13-moby #1 SMP Tue Mar 21 21:21:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-01 exited with ERRORS at Tue Jul 19 17:36:07 UTC 2022 For more details, see the log file /out/sourcedata/freesurfer/sub-01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Standard error: Return code: 1