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 = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon1
environ = {}
expert = <undefined>
flags = <undefined>
hemi = <undefined>
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
steps = <undefined>
subject_id = recon_all
subjects_dir = <undefined>
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>

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 -i /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-01_ses-01_T1w_template.nii.gz -noskullstrip -hires -openmp 8 -subjid sub-01 -sd /out/sourcedata/freesurfer -expert /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
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
Linux 09473d80fb95 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/sourcedata/freesurfer/sub-01/scripts/recon-all.local-copy'
/out/sourcedata/freesurfer/sub-01

 mri_convert /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-01_ses-01_T1w_template.nii.gz /out/sourcedata/freesurfer/sub-01/mri/orig/001.mgz 

mri_convert.bin /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-01_ses-01_T1w_template.nii.gz /out/sourcedata/freesurfer/sub-01/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_merge/sub-01_ses-01_T1w_template.nii.gz...
TR=6000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /out/sourcedata/freesurfer/sub-01/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed Aug  3 17:07:44 UTC 2022
Found 1 runs
/out/sourcedata/freesurfer/sub-01/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /out/sourcedata/freesurfer/sub-01/mri/orig/001.mgz /out/sourcedata/freesurfer/sub-01/mri/rawavg.mgz 

/out/sourcedata/freesurfer/sub-01

 mri_convert /out/sourcedata/freesurfer/sub-01/mri/rawavg.mgz /out/sourcedata/freesurfer/sub-01/mri/orig.mgz --conform_min 

mri_convert.bin /out/sourcedata/freesurfer/sub-01/mri/rawavg.mgz /out/sourcedata/freesurfer/sub-01/mri/orig.mgz --conform_min 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/sourcedata/freesurfer/sub-01/mri/rawavg.mgz...
TR=6000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /out/sourcedata/freesurfer/sub-01/mri/orig.mgz...

 mri_add_xform_to_header -c /out/sourcedata/freesurfer/sub-01/mri/transforms/talairach.xfm /out/sourcedata/freesurfer/sub-01/mri/orig.mgz /out/sourcedata/freesurfer/sub-01/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Wed Aug  3 17:07:58 UTC 2022
/out/sourcedata/freesurfer/sub-01/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/out/sourcedata/freesurfer/sub-01/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux 09473d80fb95 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Wed Aug  3 17:07:59 UTC 2022
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.970
/out/sourcedata/freesurfer/sub-01/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.970/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.970/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=6000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.970/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Aug  3 17:08:09 UTC 2022
nu_correct -clobber ./tmp.mri_nu_correct.mni.970/nu0.mnc ./tmp.mri_nu_correct.mni.970/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.970/0/ -iterations 1000 -distance 50
[root@09473d80fb95:/out/sourcedata/freesurfer/sub-01/mri/] [2022-08-03 17:08:09] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.970/0/ ./tmp.mri_nu_correct.mni.970/nu0.mnc ./tmp.mri_nu_correct.mni.970/nu1.imp

Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Number of iterations: 13 
CV of field change: 0.000988544
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.970/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.970/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.970/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Aug  3 17:09:14 UTC 2022
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at Wed Aug 3 17:09:14 UTC 2022
Ended   at Wed Aug  3 17:09:58 UTC 2022
talairach_avi done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Wed Aug  3 17:10:00 UTC 2022
/out/sourcedata/freesurfer/sub-01/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

INFO: Retrying Talairach align using 3T-based atlas...

#--------------------------------------------
#@# Talairach Wed Aug  3 17:10:00 UTC 2022
/out/sourcedata/freesurfer/sub-01/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/out/sourcedata/freesurfer/sub-01/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux 09473d80fb95 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Wed Aug  3 17:10:00 UTC 2022
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.8613
/out/sourcedata/freesurfer/sub-01/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8613/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8613/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=6000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.8613/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Aug  3 17:10:11 UTC 2022
nu_correct -clobber ./tmp.mri_nu_correct.mni.8613/nu0.mnc ./tmp.mri_nu_correct.mni.8613/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8613/0/ -iterations 1000 -distance 50
[root@09473d80fb95:/out/sourcedata/freesurfer/sub-01/mri/] [2022-08-03 17:10:11] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8613/0/ ./tmp.mri_nu_correct.mni.8613/nu0.mnc ./tmp.mri_nu_correct.mni.8613/nu1.imp

Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Processing:.................................................................................Done
Number of iterations: 13 
CV of field change: 0.000988544
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.8613/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.8613/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.8613/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Aug  3 17:11:16 UTC 2022
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 

talairach_avi log file is transforms/talairach_avi.log...
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Linux 09473d80fb95 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-01 exited with ERRORS at Wed Aug  3 17:11:41 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