Hi Rachel,
I don’t think this is the recon-all.log for the problem that you described in the first email.
I do see an error in your attached log. In the attached log, you ran processing on fsaverage subject. My understanding is that fsaverage serves as a common template.
It looks like you ran recon-all with different SUBJECTS_DIR settings. Did you get all output from one single recon-all.log? I don’t know how your system is setup. I’m wondering how the output ended up in the same log.
setenv SUBJECTS_DIR /autofs/space/minerva_001/users/nicks/dev/distribution/average
setenv SUBJECTS_DIR /autofs/space/tinia_001/users/nicks/subjects
setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
The error happened when you have SUBJECTS_DIR set to /autofs/space/tinia_001/users/nicks/subjects:
ERROR: loading filled /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/filled.mgz
SUBJECTS_DIR is the root directory for your recon-all processed data. It is a good idea to keep it separate from you Freesurfer install directory.
Can you attach the log as an attachment next time?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Rachel Wagner
Sent: Friday, February 3, 2023 11:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Directory not set properly?
External Email - Use Caution
Hello Yujing,
Thank you for your help! I have the files located in that directory (if that’s what you meant?)
Here is the system log for recon-all: (wasn’t sure what would be relevant so I included it all!)
Tue Apr 28 01:24:00 EDT 2009
/autofs/space/minerva_001/users/nicks/dev/distribution/average/fsaverage
/space/minerva/1/users/nicks/freesurfer/bin/recon-all
-s fsaverage -cortparc
subjid fsaverage
setenv SUBJECTS_DIR /autofs/space/minerva_001/users/nicks/dev/distribution/average
FREESURFER_HOME /space/minerva/1/users/nicks/freesurfer
Actual FREESURFER_HOME /autofs/space/minerva_001/users/nicks/freesurfer
build-stamp.txt: freesurfer-x86_64-redhat-linux-gnu-dev4-20090216
Linux minerva 2.6.9-78.0.13.ELsmp #1 SMP Wed Jan 14 15:55:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 65536
total used free shared buffers cached
Mem: 7403128 6807536 595592 0 133040 6185568
Swap: 16386292 224 16386068
########################################
program versions used
$Id: recon-all,v 1.201 2009/04/22 22:24:48 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.8 2008/02/29 20:14:51 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:00-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_convert.c,v 1.156 2009/01/28 20:04:23 fischl Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.4.2b
$Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $
mri_convert --version
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:00-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: tkregister2.c,v 1.104 2009/02/13 21:36:16 greve
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:01-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_normalize.c,v 1.56 2008/12/06 18:22:09 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:01-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_watershed.cpp,v 1.72 2007/11/18 22:40:49 nicks
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:02-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:02-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_label2label.c,v 1.37 2008/12/01 20:02:01 greve
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:02-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_em_register.c,v 1.63 2009/02/05 15:22:59 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:03-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_ca_normalize.c,v 1.43 2008/12/11 22:01:41
fischl Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:03-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_ca_register.c,v 1.65 2008/03/01 22:43:16 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:03-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_ca_label.c,v 1.87 2008/08/08 16:04:08 fischl Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:04-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
unknown option -ALL-INFO
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:04-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User:
nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:05-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:05-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:05-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:06-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_smooth.c,v 1.23 2007/11/23 20:39:13 nicks Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:06-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_inflate.c,v 1.38 2008/04/22 19:45:50 nicks Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:06-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:07-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_sphere.c,v 1.48 2008/03/01 01:45:18 fischl Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:07-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:08-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:08-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:08-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:09-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_make_surfaces.c,v 1.109 2009/02/05 13:46:04
fischl Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:09-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_register.c,v 1.53 2008/07/30 16:44:17 fischl
Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:09-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_anatomical_stats.c,v 1.59 2009/01/15
01:36:06 greve Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:09-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp
$ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/04/28-05:24:10-GMT BuildTimeStamp: Jan 14 2009 16:52:12 CVS: $Id: mris_curvature_stats.c,v 1.57 2009/02/04 20:58:28
nicks Exp $ User: nicks Machine: minerva Platform: Linux PlatformVersion: 2.6.9-78.0.13.ELsmp CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
#######################################
#-----------------------------------------
#@# Cortical Parc lh Tue Apr 28 01:24:10 EDT 2009
/autofs/space/minerva_001/users/nicks/dev/distribution/average/fsaverage/scripts
mris_ca_label -aseg ../mri/aseg.mgz fsaverage lh ../surf/lh.sphere.reg /space/minerva/1/users/nicks/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ../label/lh.aparc.annot
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $
$Id: mrisurf.c,v 1.625 2009/02/05 13:45:01 fischl Exp $
reading group avg surface area 822 cm^2 from file
reading atlas from /space/minerva/1/users/nicks/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs...
reading color table from GCSA file....
average std = 1.0 using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1957 labels changed using aseg
relabeling using gibbs priors...
000: 3583 changed, 163842 examined...
001: 843 changed, 15213 examined...
002: 227 changed, 4631 examined...
003: 63 changed, 1368 examined...
004: 36 changed, 408 examined...
005: 15 changed, 227 examined...
006: 8 changed, 93 examined...
007: 5 changed, 48 examined...
008: 3 changed, 29 examined...
009: 2 changed, 17 examined...
010: 2 changed, 14 examined...
011: 3 changed, 10 examined...
012: 1 changed, 13 examined...
013: 0 changed, 7 examined...
353 labels changed using aseg
000: 81 total segments, 45 labels (274 vertices) changed
001: 37 total segments, 1 labels (1 vertices) changed
002: 36 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
writing output to ../label/lh.aparc.annot...
writing colortable into annotation file...
classification took 0 minutes and 53 seconds.
#-----------------------------------------
#@# Cortical Parc rh Tue Apr 28 01:25:03 EDT 2009
/autofs/space/minerva_001/users/nicks/dev/distribution/average/fsaverage/scripts
mris_ca_label -aseg ../mri/aseg.mgz fsaverage rh ../surf/rh.sphere.reg /space/minerva/1/users/nicks/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ../label/rh.aparc.annot
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $
$Id: mrisurf.c,v 1.625 2009/02/05 13:45:01 fischl Exp $
reading group avg surface area 822 cm^2 from file
reading atlas from /space/minerva/1/users/nicks/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs...
reading color table from GCSA file....
average std = 0.7 using min determinant for regularization = 0.006
0 singular and 311 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1704 labels changed using aseg
relabeling using gibbs priors...
000: 3393 changed, 163842 examined...
001: 770 changed, 14537 examined...
002: 189 changed, 4423 examined...
003: 81 changed, 1161 examined...
004: 34 changed, 507 examined...
005: 14 changed, 217 examined...
006: 5 changed, 80 examined...
007: 1 changed, 30 examined...
008: 1 changed, 7 examined...
009: 0 changed, 7 examined...
252 labels changed using aseg
000: 90 total segments, 54 labels (309 vertices) changed
001: 37 total segments, 1 labels (2 vertices) changed
002: 36 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
writing output to ../label/rh.aparc.annot...
writing colortable into annotation file...
classification took 0 minutes and 55 seconds.
#------------------------------------------
recon-all finished without error at Tue Apr 28 01:25:58 EDT 2009
New invocation of recon-all
Fri Jan 15 15:27:24 EST 2010
/autofs/space/tinia_001/users/nicks/subjects/fsaverage
/autofs/space/terrier_001/users/nicks/freesurfer/bin/recon-all
-s fsaverage -aparc2aseg -wmparc
subjid fsaverage
setenv SUBJECTS_DIR /autofs/space/tinia_001/users/nicks/subjects
FREESURFER_HOME /autofs/space/terrier_001/users/nicks/freesurfer
Actual FREESURFER_HOME /autofs/space/terrier_001/users/nicks/freesurfer
build-stamp.txt: freesurfer-x86_64-redhat-linux-gnu-dev4-20100112
Linux terrier 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 201728
total used free shared buffers cached
Mem: 24688644 24564792 123852 0 346540 22936336
-/+ buffers/cache: 1281916 23406728
Swap: 8393920 284 8393636
########################################
program versions used
$Id: recon-all,v 1.261 2010/01/12 20:14:27 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.9 2009/10/01 17:57:09 mreuter Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:24-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_convert.c,v 1.164 2009/10/19 20:54:57 greve Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.6 2009/06/24 22:02:02 nicks Exp $
mri_convert --version
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:24-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: tkregister2.c,v 1.113 2010/01/04 18:44:42 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 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 2005-11-15 at 20:37:35
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:25-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:25-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_watershed.cpp,v 1.77 2009/09/30 20:49:06 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:25-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_gcut.cpp,v 1.4 2009/09/14 18:31:27 nicks Exp $ User:
nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:25-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:26-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_label2label.c,v 1.38 2009/11/13 18:42:10 greve
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:26-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_em_register.c,v 1.64 2010/01/05 19:22:59 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:26-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_ca_normalize.c,v 1.47 2009/07/24 19:51:58
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:27-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_ca_register.c,v 1.69 2010/01/05 18:32:47 rge21
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:27-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:27-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
unknown option -ALL-INFO
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:27-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User:
nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:28-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:28-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:28-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:28-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_smooth.c,v 1.23 2007/11/23 20:39:13 nicks Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:29-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_inflate.c,v 1.38 2008/04/22 19:45:50 nicks Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:29-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:29-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_sphere.c,v 1.49 2009/11/19 19:04:20 fischl Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:29-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:30-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:30-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:30-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:30-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_make_surfaces.c,v 1.111 2009/11/19 18:35:00
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:31-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_register.c,v 1.55 2009/11/13 19:21:43 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:31-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_anatomical_stats.c,v 1.62 2009/10/13
20:56:13 ohinds Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:31-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:31-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mris_curvature_stats.c,v 1.59 2009/08/06 16:09:49
rudolph Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.25 2009/10/13 21:41:36 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:32-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_robust_register.cpp,v 1.25 2009/10/13 21:41:36
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.13 2009/10/13 21:41:36 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:32-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_robust_template.cpp,v 1.13 2009/10/13 21:41:36
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:32-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User:
nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:32-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: nicks
Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/01/15-20:27:33-GMT BuildTimeStamp: Jan 12 2010 17:35:29 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10
18:59:24 fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /autofs/space/terrier_001/users/nicks/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /autofs/space/terrier_001/users/nicks/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
#######################################
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /autofs/space/terrier_001/users/nicks/freesurfer
Previous: /space/minerva/1/users/nicks/freesurfer
#-----------------------------------------
#@# AParc-to-ASeg Fri Jan 15 15:27:34 EST 2010
/autofs/space/tinia_001/users/nicks/subjects/fsaverage
mri_aparc2aseg --s fsaverage --volmask
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
SUBJECTS_DIR /autofs/space/tinia_001/users/nicks/subjects
subject fsaverage
outvol /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white
Reading lh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial
Loading lh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/lh.aparc.annot
Reading rh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white
Reading rh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial
Loading rh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/rh.aparc.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
-------------------------
Labeling Slice
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337762
Used brute-force search on 0 voxels
Writing output aseg to /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aparc+aseg.mgz
/autofs/space/tinia_001/users/nicks/subjects/fsaverage
mri_aparc2aseg --s fsaverage --volmask --a2009s
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
SUBJECTS_DIR /autofs/space/tinia_001/users/nicks/subjects
subject fsaverage
outvol /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0
Reading lh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white
Reading lh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial
Loading lh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/lh.aparc.a2009s.annot
Reading rh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white
Reading rh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial
Loading rh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/rh.aparc.a2009s.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
-------------------------
Labeling Slice
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337762
Used brute-force search on 0 voxels
Writing output aseg to /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Jan 15 15:30:10 EST 2010
/autofs/space/tinia_001/users/nicks/subjects/fsaverage
mri_aparc2aseg --s fsaverage --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white.avg.area.mgh
Reading in average area /autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial.avg.area.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
mghRead(/autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/filled.mgz, -1): could not open file
SUBJECTS_DIR /autofs/space/tinia_001/users/nicks/subjects
subject fsaverage
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/aparc+aseg.mgz
Reading lh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.white
Reading lh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/lh.pial
Loading lh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/lh.aparc.annot
Reading rh white surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.white
Reading rh pial surface
/autofs/space/tinia_001/users/nicks/subjects/fsaverage/surf/rh.pial
Loading rh annotations from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/label/rh.aparc.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/ribbon.mgz
Loading filled from /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/filled.mgz
ERROR: loading filled /autofs/space/tinia_001/users/nicks/subjects/fsaverage/mri/filled.mgz
Linux terrier 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Jan 15 15:30:21 EST 2010
New invocation of recon-all
Thu Dec 30 17:34:43 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage
/usr/local/freesurfer/stable5/bin/recon-all
-s fsaverage -cortparc
subjid fsaverage
setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer/stable5
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20101225
Linux terrier 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 201728
total used free shared buffers cached
Mem: 24688596 1544140 23144456 0 91544 899412
-/+ buffers/cache: 553184 24135412
Swap: 8393920 16 8393904
########################################
program versions used
$Id: recon-all,v 1.313.2.32 2010/12/30 19:11:13 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:43-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:43-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: tkregister2.c,v 1.117.2.3 2010/11/22 22:57:46
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
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: 2010/12/30-22:34:44-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_make_uchar.c,v 1.2.2.3 2010/12/09 21:16:54
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:44-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_normalize.c,v 1.65.2.1 2010/11/13 20:05:25
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:44-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_watershed.cpp,v 1.81.2.2 2010/11/11 20:31:14
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:44-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_gcut.cpp,v 1.7.2.2 2010/12/08 14:16:10 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:44-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:45-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:45-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_em_register.c,v 1.77.2.2 2010/08/26
04:12:35 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:45-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:45-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:46-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:46-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:46-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:46-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:47-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_concatenate_lta.c,v 1.5.2.1 2010/11/11
21:06:39 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:47-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_normalize_tp2.c,v 1.6.4.1 2010/11/11
21:22:33 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:47-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:47-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:47-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:48-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:48-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27
23:37:16 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:48-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:48-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:49-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:49-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_make_surfaces.c,v 1.113.2.6 2010/12/13
20:42:42 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:49-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:49-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19
krish Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:50-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28
20:36:45 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:50-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:50-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_curvature_stats.c,v 1.60.2.1 2010/12/10
03:14:32 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:50-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.31.2.4 2010/12/12 20:21:18 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:50-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_robust_register.cpp,v 1.31.2.4 2010/12/12
20:21:18 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.18.2.7 2010/12/17 23:37:39 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:51-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_robust_template.cpp,v 1.18.2.7 2010/12/17
23:37:39 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:51-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $
User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:51-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User:
nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:51-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10
18:59:24 fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:34:51-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/freesurfer/stable5/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/stable5/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#-----------------------------------------
#@# Cortical Parc lh Thu Dec 30 17:34:52 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $
$Id: mrisurf.c,v 1.678.2.2 2010/12/09 23:08:48 nicks Exp $
reading atlas from /usr/local/freesurfer/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 1.0 using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1957 labels changed using aseg
relabeling using gibbs priors...
000: 3485 changed, 163842 examined...
001: 767 changed, 15075 examined...
002: 190 changed, 4410 examined...
003: 72 changed, 1190 examined...
004: 36 changed, 441 examined...
005: 23 changed, 232 examined...
006: 7 changed, 131 examined...
007: 4 changed, 41 examined...
008: 0 changed, 20 examined...
336 labels changed using aseg
000: 160 total segments, 113 labels (368 vertices) changed
001: 52 total segments, 5 labels (9 vertices) changed
002: 47 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 13 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1970 vertices marked for relabeling...
1968 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 47 seconds.
#-----------------------------------------
#@# Cortical Parc rh Thu Dec 30 17:35:38 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $
$Id: mrisurf.c,v 1.678.2.2 2010/12/09 23:08:48 nicks Exp $
reading atlas from /usr/local/freesurfer/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 0.7 using min determinant for regularization = 0.006
0 singular and 311 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1704 labels changed using aseg
relabeling using gibbs priors...
000: 3389 changed, 163842 examined...
001: 696 changed, 14493 examined...
002: 164 changed, 4083 examined...
003: 63 changed, 991 examined...
004: 23 changed, 403 examined...
005: 8 changed, 149 examined...
006: 6 changed, 52 examined...
007: 2 changed, 40 examined...
008: 2 changed, 10 examined...
009: 1 changed, 10 examined...
010: 0 changed, 7 examined...
209 labels changed using aseg
000: 128 total segments, 89 labels (451 vertices) changed
001: 42 total segments, 3 labels (4 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1689 vertices marked for relabeling...
1689 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 47 seconds.
#------------------------------------------
recon-all -s fsaverage finished without error at Thu Dec 30 17:36:25 EST 2010
New invocation of recon-all
Thu Dec 30 17:40:00 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage
/usr/local/freesurfer/stable5/bin/recon-all
-s fsaverage -cortparc2
subjid fsaverage
setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer/stable5
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20101225
Linux terrier 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 201728
total used free shared buffers cached
Mem: 24688596 1861720 22826876 0 91920 1214756
-/+ buffers/cache: 555044 24133552
Swap: 8393920 16 8393904
########################################
program versions used
$Id: recon-all,v 1.313.2.32 2010/12/30 19:11:13 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:01-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:01-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: tkregister2.c,v 1.117.2.3 2010/11/22 22:57:46
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
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: 2010/12/30-22:40:01-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_make_uchar.c,v 1.2.2.3 2010/12/09 21:16:54
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:01-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_normalize.c,v 1.65.2.1 2010/11/13 20:05:25
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:02-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_watershed.cpp,v 1.81.2.2 2010/11/11 20:31:14
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:03-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_gcut.cpp,v 1.7.2.2 2010/12/08 14:16:10 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:03-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:03-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_em_register.c,v 1.77.2.2 2010/08/26
04:12:35 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03
mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:04-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_concatenate_lta.c,v 1.5.2.1 2010/11/11
21:06:39 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_normalize_tp2.c,v 1.6.4.1 2010/11/11
21:22:33 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27
23:37:16 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10
nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_make_surfaces.c,v 1.113.2.6 2010/12/13
20:42:42 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04
fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19
krish Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28
20:36:45 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl
Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_curvature_stats.c,v 1.60.2.1 2010/12/10
03:14:32 nicks Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp
$ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.31.2.4 2010/12/12 20:21:18 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_robust_register.cpp,v 1.31.2.4 2010/12/12
20:21:18 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.18.2.7 2010/12/17 23:37:39 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_robust_template.cpp,v 1.18.2.7 2010/12/17
23:37:39 mreuter Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $
User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User:
nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10
18:59:24 fischl Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/12/30-22:40:05-GMT BuildTimeStamp: Dec 25 2010 11:43:50 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29
greve Exp $ User: nicks Machine: terrier Platform: Linux PlatformVersion: 2.6.18-194.8.1.el5 CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/freesurfer/stable5/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/stable5/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Dec 30 17:40:05 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $
$Id: mrisurf.c,v 1.678.2.2 2010/12/09 23:08:48 nicks Exp $
reading atlas from /usr/local/freesurfer/stable5/average/lh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 3.9 0.2 using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
137 labels changed using aseg
relabeling using gibbs priors...
000: 9948 changed, 163842 examined...
001: 2209 changed, 38389 examined...
002: 667 changed, 11662 examined...
003: 251 changed, 3773 examined...
004: 111 changed, 1490 examined...
005: 54 changed, 678 examined...
006: 30 changed, 315 examined...
007: 22 changed, 172 examined...
008: 13 changed, 116 examined...
009: 4 changed, 65 examined...
010: 3 changed, 26 examined...
011: 2 changed, 21 examined...
012: 1 changed, 10 examined...
013: 1 changed, 7 examined...
014: 1 changed, 7 examined...
015: 0 changed, 7 examined...
56 labels changed using aseg
000: 263 total segments, 182 labels (1583 vertices) changed
001: 88 total segments, 7 labels (47 vertices) changed
002: 81 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 37 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
285 vertices marked for relabeling...
285 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 52 seconds.
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Dec 30 17:40:58 EST 2010
/autofs/cluster/freesurfer/subjects/fsaverage/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $
$Id: mrisurf.c,v 1.678.2.2 2010/12/09 23:08:48 nicks Exp $
reading atlas from /usr/local/freesurfer/stable5/average/rh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 1.9 0.2 using min determinant for regularization = 0.000
0 singular and 851 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
26 labels changed using aseg
relabeling using gibbs priors...
000: 10632 changed, 163842 examined...
001: 2221 changed, 40264 examined...
002: 659 changed, 11771 examined...
003: 245 changed, 3831 examined...
004: 97 changed, 1470 examined...
005: 47 changed, 592 examined...
006: 17 changed, 282 examined...
007: 7 changed, 103 examined...
008: 2 changed, 43 examined...
009: 1 changed, 14 examined...
010: 0 changed, 7 examined...
23 labels changed using aseg
000: 273 total segments, 194 labels (2011 vertices) changed
001: 94 total segments, 14 labels (136 vertices) changed
002: 80 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 59 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
250 vertices marked for relabeling...
250 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 52 seconds.
#------------------------------------------
recon-all -s fsaverage finished without error at Thu Dec 30 17:41:50 EST 2010
From: Huang, Yujing
Sent: February 3, 2023 11:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Directory not set properly?
Hi Rachel,
Can you check if you have access to the input files?
ls -l /usr/home/developer/desktop/TIWI.nii
ls -l /usr/home/developer/desktop/T2_Flair.nii
Can you attach recon-all.log?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Rachel Wagner
Sent: Friday, February 3, 2023 10:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Directory not set properly?
External Email - Use Caution
Hello,
I am trying to run recon-all on my data and am encountering the following issue:
developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i /usr/home/developer/desktop/TIWI.nii -T2 /usr/home/developer/desktop/T2_Flair.nii -T2pial -all
ERROR: cannot find /usr/home/developer/desktop/TIWI.nii
Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3T00300 exited with ERRORS at Fri Feb 3 10:49:02 EST 2023
For more details, see the log file
To report a problem, see
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i sample-001.mgz
ERROR: cannot find sample-001.mgz
Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3T00300 exited with ERRORS at Fri Feb 3 10:52:53 EST 2023
For more details, see the log file
To report a problem, see
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
developer@developer-VirtualBox:~/freesurfer$
Is it that my path is not set correctly?
Thank you!
Rachel Wagner