Error: Node Name: _autorecon_surfs0

tali.weiss · September 27, 2021, 5:53am

I have an error in recon-all. It run in Ubuntu 20.04.2.
It did work with a single subject (without the for loop), so I assume it is a memory issue? I thought it run a single subject in each iteration.

for i in cat $bids_root/subjects_list.txt; do
echo $i

fmriprep-docker $bids_root $out participant
–fs-license-file /home/taliw/data/derivatives/license.txt
–skip_bids_validation
–participant-label $i
–md-only-boilerplate
–nthreads 4
–error-on-aroma-warnings
–ignore {fieldmaps,slicetiming,sbref,t2w,flair}
–output-spaces MNI152NLin2009cAsym:res-2
–dummy-scans 5
–use-aroma
–fd-spike-threshold 0.25
–stop-on-first-crash
–resource-monitor
–write-graph

done

Node Name: _autorecon_surfs0

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 428, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 822, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 753, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 3 -subjid sub-005 -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 1e7f2c054df0 5.8.0-53-generic #60~20.04.1-Ubuntu SMP Thu May 6 09:52:46 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
‘/opt/freesurfer/bin/recon-all’ → ‘/out/freesurfer/sub-005/scripts/recon-all.local-copy’
#--------------------------------------------
#@# Tessellate lh Thu Sep 23 20:53:30 UTC 2021
/out/freesurfer/sub-005/scripts

mri_pretess …/mri/filled.mgz 255 …/mri/norm.mgz …/mri/filled-pretess255.mgz

Iteration Number : 1
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 4 found - 4 modified | TOTAL: 4
pass 2 (yz+): 0 found - 4 modified | TOTAL: 4
pass 1 (yz-): 1 found - 1 modified | TOTAL: 5
pass 2 (yz-): 0 found - 1 modified | TOTAL: 5
pass 1 (xz+): 0 found - 0 modified | TOTAL: 5
pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (±): 1 found - 1 modified | TOTAL: 1
pass 2 (±): 0 found - 1 modified | TOTAL: 1
pass 1 (–): 0 found - 0 modified | TOTAL: 1
pass 1 (-+): 0 found - 0 modified | TOTAL: 1
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (±): 0 found - 0 modified | TOTAL: 0
pass 1 (–): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0

Total Number of Modified Voxels = 6 (out of 221490: 0.002709)
Ambiguous edge configurations…

mri_pretess done

mri_tessellate …/mri/filled-pretess255.mgz 255 …/surf/lh.orig.nofix

Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp
Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp
slice 40: 1849 vertices, 2020 faces
slice 50: 8286 vertices, 8569 faces
slice 60: 17957 vertices, 18318 faces
slice 70: 28353 vertices, 28702 faces
slice 80: 38488 vertices, 38800 faces
slice 90: 48688 vertices, 49059 faces
slice 100: 59017 vertices, 59358 faces
slice 110: 68799 vertices, 69143 faces
slice 120: 78494 vertices, 78842 faces
slice 130: 87986 vertices, 88328 faces
slice 140: 96797 vertices, 97080 faces
slice 150: 104573 vertices, 104849 faces
slice 160: 111057 vertices, 111267 faces
slice 170: 116342 vertices, 116492 faces
slice 180: 119738 vertices, 119830 faces
slice 190: 120480 vertices, 120494 faces
slice 200: 120480 vertices, 120494 faces
slice 210: 120480 vertices, 120494 faces
slice 220: 120480 vertices, 120494 faces
slice 230: 120480 vertices, 120494 faces
slice 240: 120480 vertices, 120494 faces
slice 250: 120480 vertices, 120494 faces
using the conformed surface RAS to save vertex points…
writing …/surf/lh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;

rm -f …/mri/filled-pretess255.mgz

mris_extract_main_component …/surf/lh.orig.nofix …/surf/lh.orig.nofix

counting number of connected components…
120480 voxel in cpt #1: X=-14 [v=120480,e=361482,f=240988] located at (-23.462450, -25.882595, 29.635824)
For the whole surface: X=-14 [v=120480,e=361482,f=240988]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Sep 23 20:53:32 UTC 2021
/out/freesurfer/sub-005/scripts

mris_smooth -nw -seed 1234 …/surf/lh.orig.nofix …/surf/lh.smoothwm.nofix

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations…
smoothing complete - recomputing first and second fundamental forms…
#--------------------------------------------
#@# Inflation1 lh Thu Sep 23 20:53:35 UTC 2021
/out/freesurfer/sub-005/scripts

mris_inflate -no-save-sulc …/surf/lh.smoothwm.nofix …/surf/lh.inflated.nofix

Not saving sulc
Reading …/surf/lh.smoothwm.nofix
avg radius = 44.7 mm, total surface area = 63931 mm^2
writing inflated surface to …/surf/lh.inflated.nofix
inflation took 0.2 minutes

step 000: RMS=0.151 (target=0.015)
step 005: RMS=0.112 (target=0.015)
step 010: RMS=0.081 (target=0.015)
step 015: RMS=0.067 (target=0.015)
step 020: RMS=0.056 (target=0.015)
step 025: RMS=0.048 (target=0.015)
step 030: RMS=0.041 (target=0.015)
step 035: RMS=0.036 (target=0.015)
step 040: RMS=0.033 (target=0.015)
step 045: RMS=0.031 (target=0.015)
step 050: RMS=0.029 (target=0.015)
step 055: RMS=0.028 (target=0.015)
step 060: RMS=0.027 (target=0.015)
inflation complete.
Not saving sulc
mris_inflate utimesec 25.935448
mris_inflate stimesec 0.116033
mris_inflate ru_maxrss 187068
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 45265
mris_inflate ru_majflt 0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 8480
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 21990
mris_inflate ru_nivcsw 59
#--------------------------------------------
#@# QSphere lh Thu Sep 23 20:53:45 UTC 2021
/out/freesurfer/sub-005/scripts

mris_sphere -q -seed 1234 …/surf/lh.inflated.nofix …/surf/lh.qsphere.nofix

doing quick spherical unfolding.
setting seed for random number genererator to 1234
Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp
Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp
reading original vertex positions…
unfolding cortex into spherical form…
surface projected - minimizing metric distortion…
vertex spacing 1.05 ± 0.59 (0.00–>6.54) (max @ vno 52577 → 53632)
face area 0.03 ± 0.04 (-0.11–>0.66)
Segmentation fault (core dumped)
Linux 1e7f2c054df0 5.8.0-53-generic #60~20.04.1-Ubuntu SMP Thu May 6 09:52:46 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-005 exited with ERRORS at Thu Sep 23 20:54:26 UTC 2021

For more details, see the log file /out/freesurfer/sub-005/scripts/recon-all-lh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

Steven · September 27, 2021, 1:11pm

Segmentation faults, as in the error message, could be due to memory issues or due to the code trying to access memory it does not have access to (e.g. accessing a drive you do not have permission to read). If the same command worked outside the loop then I would guess it’s a memory issue, so try devoting more RAM to the task.