External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to convert my .nii files (taken from ADNI dataset) to
subject files (like bert). For the same I'm following this website :
https://secure-web.cisco.com/13_r_7kEeP_WS7SHxH0ECZXOxZuTEltmsSnlVNl81ZLfHEwNDB_11o3EFmEh8jBnC1DRib-gmQgxCzrNA2y7JAD-w_LU7bDv24QbcO5MeKe-gTkgaWnqJg26eUtDBwGTLk0S36S5lkRrXmCRiZB0Vo5JcvmWKq_fXgBxxGfdTbGXfKQG6TpTcO-fj934vAZik-fcyNAA495Ukja-dZgVLE2Acueds8sqLHs1zmUM1G3CIh9Bi3Y9Z1xozoa5FC1GnJHhYJKCLOw4GoZkdKRTaFQ/https%3A%2F%2Fneuroimage.usc.edu%2Fbrainstorm%2FTutorials%2FLabelFreeSurfer
I'm getting an error while performing step 4 of 'Running Freesurfer'
heading.
Command that is giving error : recon-all -all -subjid <subject_id>
Here my <subject_id> is subject_0295
Error on the terminal : recon-all -s subject_0295 exited with ERRORS at Tue
Dec 8 18:25:40 IST 2020
The freesurfer/subjects/subject_0295/scripts/recon-all.log file didn't
mention any specific error.
I've searched the list and no similar errors have been reported. Does
anyone have any thoughts on how to trouble-shoot this one? Also, I have
attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Ubuntu 16.04.7 LTS
3) recon-all.log: see attached
--
Regards,
Ms. Devanshi Jain
Tue Dec 8 17:55:11 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
/media/ayushi/TI10716000E/freesurfer/bin/recon-all
-i mri_0295.nii -subjid subject_0295
subjid subject_0295
setenv SUBJECTS_DIR /media/ayushi/TI10716000E/freesurfer/subjects
FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
Actual FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 31172
maxlocks unlimited
maxsignal 31172
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 8085540 1588064 5009496 212356 1487980 5975464
Swap: 8306684 0 8306684
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/ayushi/TI10716000E/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/ayushi/TI10716000E/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/mri_0295.nii /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig/001.mgz
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/mri_0295.nii /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/ayushi/TI10716000E/freesurfer/subjects/mri_0295.nii...
TR=0.00, 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 /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig/001.mgz...
#------------------------------------------
Started at Tue Dec 8 17:55:11 IST 2020
Ended at Tue Dec 8 17:55:18 IST 2020
#@#%# recon-all-run-time-hours 0.002
recon-all -s subject_0295 finished without error at Tue Dec 8 17:55:19 IST 2020
New invocation of recon-all
Tue Dec 8 17:55:46 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
/media/ayushi/TI10716000E/freesurfer/bin/recon-all
-all -subjid subject_0295
subjid subject_0295
setenv SUBJECTS_DIR /media/ayushi/TI10716000E/freesurfer/subjects
FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
Actual FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 31172
maxlocks unlimited
maxsignal 31172
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 8085540 1593776 4615952 220768 1875812 5960472
Swap: 8306684 0 8306684
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:25:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/ayushi/TI10716000E/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/ayushi/TI10716000E/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Tue Dec 8 17:55:49 IST 2020
Found 1 runs
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/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 /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig/001.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz --conform
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz...
TR=0.00, 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)
Original Data has (1.2, 0.9375, 0.9375) mm size and (166, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz...
mri_add_xform_to_header -c /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/transforms/talairach.xfm /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Dec 8 17:55:57 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subject_0295 exited with ERRORS at Tue Dec 8 17:56:00 IST 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
New invocation of recon-all
Tue Dec 8 18:25:27 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
/media/ayushi/TI10716000E/freesurfer/bin/recon-all
-all -subjid subject_0295
subjid subject_0295
setenv SUBJECTS_DIR /media/ayushi/TI10716000E/freesurfer/subjects
FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
Actual FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 31172
maxlocks unlimited
maxsignal 31172
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 8085540 1933900 3871028 366956 2280612 5465932
Swap: 8306684 0 8306684
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/12/08-12:55:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: ayushi Machine: ayushi-Satellite-S55-C Platform: Linux PlatformVersion: 4.15.0-126-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/ayushi/TI10716000E/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/ayushi/TI10716000E/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Tue Dec 8 18:25:30 IST 2020
Found 1 runs
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/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 /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig/001.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz --conform
mri_convert /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/rawavg.mgz...
TR=0.00, 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)
Original Data has (1.2, 0.9375, 0.9375) mm size and (166, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz...
mri_add_xform_to_header -c /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/transforms/talairach.xfm /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz /media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Dec 8 18:25:38 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subject_0295 exited with ERRORS at Tue Dec 8 18:25:40 IST 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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