I am trying to run fMRIPrep and keep getting the error:
ln: failed to create symbolic link 'lh.white.H': Operation not supported
I am using a Linux machine (Ubuntu 22.04.03). I am currently running in a Docker container, I have also tried running in Apptainer/Singularity and got the same error. I removed some text from the following logs just to stay within the character limit.
Here is my Docker fMRIPrep call:
sudo docker run -ti --rm \
-v /mnt/restricted/Imaging/MRI_UW/Psil_sub-study/flywheel/nicholasgroup_PRIMUSS/SUBJECTS/BIDS:/data:ro \
-v /mnt/restricted/Imaging/MRI_UW/Psil_sub-study/flywheel/nicholasgroup_PRIMUSS/SUBJECTS/BIDS/derivatives/fmriprep:/out \
-v $HOME/EBublitz/Scratch:/work \
-v $HOME/freesurfer.txt:/opt/freesurfer/license.txt \
docker.io/poldracklab/fmriprep:latest \
--participant-label RMRCN011223 \
--nprocs 8 \
--omp-nthreads 8 \
--mem 64000 \
--dummy-scans 5 \
--output-spaces T1w \
--cifti-output 91k \
/data \
/out \
-w /work \
participant
Here is my crash log:
Node: _autorecon_surfs0
Working directory: /work/fmriprep_wf/single_subject_RMRCN011223_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0
Node inputs:
FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon-hemi
environ = {}
expert = <undefined>
flags = ['-noparcstats', '-noparcstats2', '-noparcstats3', '-nohyporelabel', '-nobalabels']
hemi = lh
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 = sub-RMRCN011223
subjects_dir = /out/freesurfer
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-RMRCN011223 -sd /out/freesurfer
Standard output:
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/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux 124f86efde9f 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-RMRCN011223/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Curv .H and .K lh Tue Dec 26 21:23:24 UTC 2023
/out/freesurfer/sub-RMRCN011223/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 21.742*4pi (273.219) --> -21 handles
ICI = 194.4, FI = 1865.4, variation=29642.747
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux 124f86efde9f 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-RMRCN011223 exited with ERRORS at Tue Dec 26 21:23:26 UTC 2023
For more details, see the log file /out/freesurfer/sub-RMRCN011223/scripts/recon-all-lh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
ln: failed to create symbolic link 'lh.white.H': Operation not supported
Return code: 1
**Here is my recon-all-lh.log:**
Tue Dec 26 20:52:30 UTC 2023
/out/freesurfer/sub-RMRCN011223
/opt/freesurfer/bin/recon-all
-autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-RMRCN011223 -sd /out/freesurfer
subjid sub-RMRCN011223
setenv SUBJECTS_DIR /out/freesurfer
FREESURFER_HOME /opt/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Linux 124f86efde9f 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1048576
memorylocked 8192 kbytes
maxproc unlimited
maxlocks unlimited
maxsignal 514126
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 131742924 8446152 43201156 201012 80095616 121177248
Swap: 2097148 0 2097148
########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
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
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2023/12/26-20:52:31-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 124f86efde9f Platform: Linux PlatformVersion: 6.2.0-37-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /opt/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /opt/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# Curv .H and .K lh Tue Dec 26 21:23:24 UTC 2023
/out/freesurfer/sub-RMRCN011223/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 21.742*4pi (273.219) --> -21 handles
ICI = 194.4, FI = 1865.4, variation=29642.747
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux 124f86efde9f 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-RMRCN011223 exited with ERRORS at Tue Dec 26 21:23:26 UTC 2023
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Sorry for the long post, if anyone could help, I would really appreciate it!