Best wishes,Dear Bruce,I apologize, I misread your last message. My fsaverage folder is now empty. We had some issues with storage space for our output files and I am rerunning a number of patients for a different study from the ones I had done previously (but acquired with the same protocol). I guess these files got lost. Is there a way I can reset my freesurfer install to function as though I am running cases for the first time / get things working again?
SalOn Tue, Jun 25, 2013 at 6:25 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
those are the contents of /mnt/glusterfs/salsoman/output/FS/fsaverage/label/lh.BA1.label?
I've attached our current one so that you can compare
cheers
Bruce
On Tue, 25 Jun 2013, Salil Soman wrote:
Thank you Doug,
Here are the file contents.
-Sal
Sun Jun 23 22:25:24 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS
/mnt/glusterfs/salsoman/freesurfer/bin/recon-all
-i SPGR/2536_21_1.nii.gz -s GK_2536_FS -nuintensitycor-3T -nocanorm -openmp
50 -all
subjid GK_2536_FS
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS
FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer
Actual FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18
16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 772831
maxlocks unlimited
maxsignal 772831
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 99005808 49579412 49426396 0 1598396 37801604
-/+ buffers/cache: 10179412 88826396
Swap: 10485756 459696 10026060
########################################
program versions used
$Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 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: 2013/06/24-05:25:24-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-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: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-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: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013
00:28:02 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $
User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56
greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 50 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013
00:28:02 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $
User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_concatenate_lta.c,v 1.10
2011/03/16 21:23:48 nicks Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34
nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07
greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform:
Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_make_surfaces.c,v
1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_anatomical_stats.c,v
1.72 2011/03/02 00:04:26 nicks Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp
$ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_curvature_stats.c,v
1.64 2011/03/02 00:04:30 nicks Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/06/24-05:25:34-GMT BuildTimeStamp: Feb 26 2013
00:28:02 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $
User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-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: 2013/06/24-05:25:35-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_register.cpp,v
1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-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: 2013/06/24-05:25:35-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_template.cpp,v
1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013
00:28:02 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User:
salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion:
3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013
00:28:02 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User:
salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion:
3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT
BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_fuse_segmentations.c,v
1.8 2011/03/02 00:04:15 nicks Exp $ User: salsoman Machine:
barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/24-05:25:36-GMT BuildTimeStamp: Feb 26
2013 00:28:02 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve
Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux
PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /mnt/glusterfs/salsoman/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /mnt/glusterfs/salsoman/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS
mri_convert /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz
mri_convert /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz...
TR=8.66, 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 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sun Jun 23 22:25:47 PDT 2013
Found 1 runs
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/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 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS
mri_convert /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz --conform
mri_convert /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz...
TR=8.66, 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 (0.8594, 0.8594, 1) mm size and (256, 256, 156) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz...
mri_add_xform_to_header -c
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach.xfm
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sun Jun 23 22:26:10 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Sun Jun 23 22:38:56 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6134,
pval=0.2817 >= threshold=0.0050)
awk -f /mnt/glusterfs/salsoman/freesurfer/bin/extract_talairach_avi_QA.awk/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach_avi.l
og
tal_QC_AZS/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach_avi.l
og
TalAviQA: 0.97859
z-score: 0
TalAviQA2: 3.3941
#--------------------------------------------
#@# Nu Intensity Correction Sun Jun 23 22:39:05 PDT 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm
--proto-iters 1000 --distance 50 --n 1
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
/mnt/glusterfs/salsoman/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000
--distance 50 --n 1
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18
16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Sun Jun 23 22:39:06 PDT 2013
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
tmpdir is ./tmp.mri_nu_correct.mni.7330
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=8.66, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.7330/nu0.mnc...
--------------------------------------------------------
Iteration 1 Sun Jun 23 22:39:17 PDT 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.7330/nu0.mnc
./tmp.mri_nu_correct.mni.7330/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.7330/0/ -iterations 1000 -distance 50
[salsoman@barley13.stanford.edu:/mnt/glusterfs/salsoman/output/FS/GK_2536_F
S/mri/] [2013-06-23 22:39:18] running:
/mnt/glusterfs/salsoman/freesurfer/mni/bin/nu_estimate_np_and_em -parzen
-log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask
-nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp
-tmpdir ./tmp.mri_nu_correct.mni.7330/0/
./tmp.mri_nu_correct.mni.7330/nu0.mnc ./tmp.mri_nu_correct.mni.7330/nu1.imp
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Use of ?PATTERN? without explicit operator is deprecated at
/mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153.
Processing:................................................................
.Done
Number of iterations: 109
CV of field change: 0.000986757
[salsoman@barley13.stanford.edu:/mnt/glusterfs/salsoman/output/FS/GK_2536_F
S/mri/] [2013-06-23 22:46:39] running:
/mnt/glusterfs/salsoman/freesurfer/mni/bin/make_template -quiet -shrink 3
./tmp.mri_nu_correct.mni.7330/nu0.mnc
./tmp.mri_nu_correct.mni.7330/0//template.mnc
Transformingslices:....................................................................
..................Done
Transformingslices:....................................................................
...........................................................................
...........................................................................
......................................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --min -1 --o
./tmp.mri_nu_correct.mni.7330/ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --min -1 --o
./tmp.mri_nu_correct.mni.7330/ones.mgz
sysname Linux
hostname barley13.stanford.edu
machine x86_64
user salsoman
input ./tmp.mri_nu_correct.mni.7330/nu1.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.7330/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i
orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf
./tmp.mri_nu_correct.mni.7330/input.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i
orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf
./tmp.mri_nu_correct.mni.7330/input.mean.dat
sysname Linux
hostname barley13.stanford.edu
machine x86_64
user salsoman
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.7330/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 16777216.000
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.7330/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i
./tmp.mri_nu_correct.mni.7330/nu1.mnc --sum
./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf
./tmp.mri_nu_correct.mni.7330/output.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i
./tmp.mri_nu_correct.mni.7330/nu1.mnc --sum
./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf
./tmp.mri_nu_correct.mni.7330/output.mean.dat
sysname Linux
hostname barley13.stanford.edu
machine x86_64
user salsoman
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.7330/ones.mgz
Loading ./tmp.mri_nu_correct.mni.7330/nu1.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 16777216.000
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.7330/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.7330/nu1.mnc
./tmp.mri_nu_correct.mni.7330/nu1.mnc mul .90527967007596602086
Saving result to './tmp.mri_nu_correct.mni.7330/nu1.mnc' (type = MINC
) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.7330/nu1.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.7330/nu1.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.7330/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 13 seconds.
mapping (11, 68) to ( 3, 110)
Sun Jun 23 22:48:17 PDT 2013
mri_nu_correct.mni done
mri_add_xform_to_header -c
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach.xfm
nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sun Jun 23 22:48:19 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
1.097 -0.025 -0.058 1.356;
0.020 1.037 0.488 -12.228;
0.025 -0.377 1.099 4.862;
0.000 0.000 0.000 1.000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 15
Starting OpenSpline(): npoints = 15
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 109
gm peak at 76 (76), valley at 58 (58)
csf peak at 38, setting threshold to 63
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 76 (76), valley at 58 (58)
csf peak at 38, setting threshold to 63
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 4 minutes and 10 seconds.
#--------------------------------------------
#@# Skull Stripping Sun Jun 23 22:52:31 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_em_register -skull nu.mgz
/mnt/glusterfs/salsoman/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta
======= NUMBER OF OPENMP THREADS = 50 =======
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading'/mnt/glusterfs/salsoman/freesurfer/average/RB_all_withskull_2008-03-26.gca
'...
average std = 23.1 using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=15.0
skull bounding box = (49, 48, 35) --> (207, 208, 231)
using (102, 101, 133) as brain centroid...
mean wm in atlas = 126, using box (83,81,109) --> (121, 120,157) to find MRI
wm
before smoothing, mri peak at 109
after smoothing, mri peak at 109, scaling input intensities by 1.156
scaling channel 0 by 1.15596
initial log_p = -4.8
************************************************
First Search limited to translation only.
************************************************
max log p = -4.714732 @ (-9.091, -9.091, -27.273)
max log p = -4.622298 @ (13.636, -4.545, 4.545)
max log p = -4.568388 @ (-2.273, -2.273, 2.273)
max log p = -4.567887 @ (-3.409, 1.136, -1.136)
max log p = -4.554366 @ (-0.568, -5.114, 0.568)
max log p = -4.554366 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -19.9, -21.0): log p = -4.554
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.6
(thresh=-4.5)
1.064 0.000 0.000 -9.830;
0.000 1.194 0.320 -71.787;
0.000 -0.320 1.194 -0.574;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.064 0.000 0.000 -9.830;
0.000 1.270 0.340 -84.084;
0.000 -0.296 1.105 7.422;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.064 0.000 0.000 -9.830;
0.000 1.270 0.340 -84.084;
0.000 -0.296 1.105 7.422;
0.000 0.000 0.000 1.000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.082 -0.052 0.020 -7.974;
0.036 1.306 0.390 -99.503;
-0.033 -0.327 1.073 19.471;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.082 -0.052 0.020 -7.974;
0.036 1.306 0.390 -99.503;
-0.033 -0.327 1.073 19.471;
0.000 0.000 0.000 1.000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.084 -0.052 0.020 -8.295;
0.035 1.296 0.416 -101.760;
-0.034 -0.358 1.062 25.483;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1
(thresh=-4.1)
1.084 -0.052 0.020 -8.295;
0.035 1.296 0.416 -101.760;
-0.034 -0.358 1.062 25.483;
0.000 0.000 0.000 1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.08441 -0.05186 0.02026 -8.29545;
0.03508 1.29640 0.41613 -101.75975;
-0.03396 -0.35825 1.06199 25.48265;
0.00000 0.00000 0.00000 1.00000;
nsamples 3481
Quasinewton: input matrix
1.08441 -0.05186 0.02026 -8.29545;
0.03508 1.29640 0.41613 -101.75975;
-0.03396 -0.35825 1.06199 25.48265;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =
-0.0 tol 0.000010
Resulting transform:
1.084 -0.052 0.020 -8.295;
0.035 1.296 0.416 -101.760;
-0.034 -0.358 1.062 25.483;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -4.1 (old=-4.8)
transform before final EM align:
1.084 -0.052 0.020 -8.295;
0.035 1.296 0.416 -101.760;
-0.034 -0.358 1.062 25.483;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 382743 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.08441 -0.05186 0.02026 -8.29545;
0.03508 1.29640 0.41613 -101.75975;
-0.03396 -0.35825 1.06199 25.48265;
0.00000 0.00000 0.00000 1.00000;
nsamples 382743
Quasinewton: input matrix
1.08441 -0.05186 0.02026 -8.29545;
0.03508 1.29640 0.41613 -101.75975;
-0.03396 -0.35825 1.06199 25.48265;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =
4.4 tol 0.000000
final transform:
1.084 -0.052 0.020 -8.295;
0.035 1.296 0.416 -101.760;
-0.034 -0.358 1.062 25.483;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta...
registration took 69 minutes and 47 seconds.
mri_watershed -T1 -brain_atlas
/mnt/glusterfs/salsoman/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for
details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=126 y=122 z=125 r=70
first estimation of the main basin volume: 1445912 voxels
Looking for seedpoints
2 found in the cerebellum
14 found in the rest of the brain
global maximum in x=105, y=117, z=92, Imax=255
CSF=21, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=10816010181 voxels, voxel volume =1.000
= 10816010181 mmm3 = 10816010.240 cm3
done.
PostAnalyze...Basin Prior
12 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=128,y=129, z=122, r=9758
iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 45874
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1030067734
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1060864313
RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=41 , nb = -1082494987
LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1100073048
OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=24 , nb = 1081747772
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 32, 43, 52, 73
after analyzing : 32, 49, 52, 55
RIGHT_CER
before analyzing : 14, 19, 40, 85
after analyzing : 14, 33, 40, 46
LEFT_CER
before analyzing : 15, 23, 44, 76
after analyzing : 15, 37, 44, 46
RIGHT_BRAIN
before analyzing : 41, 48, 52, 74
after analyzing : 41, 50, 52, 56
LEFT_BRAIN
before analyzing : 34, 45, 52, 71
after analyzing : 34, 49, 52, 54
OTHER
before analyzing : 24, 40, 66, 87
after analyzing : 24, 57, 66, 64
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...60 iterations
*********************VALIDATION*********************
curvature mean = -0.014, std = 0.013
curvature mean = 65.084, std = 6.593
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 4.44, sigma = 7.78
after rotation: sse = 4.44, sigma = 7.78
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 5.53, its var is 11.13
before Erosion-Dilatation 3.50% of inacurate vertices
after Erosion-Dilatation 4.66% of inacurate vertices
Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...46 iterations
mri_strip_skull: done peeling brain
Brain Size = 1439142 voxels, voxel volume = 1.000 mm3
= 1439142 mmm3 = 1439.142 cm3
******************************
Saving brainmask.auto.mgz
done
cp brainmask.auto.mgz brainmask.mgz
#-------------------------------------
#@# EM Registration Mon Jun 24 00:03:10 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta
======= NUMBER OF OPENMP THREADS = 50 =======
aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading
'/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9 using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 14.9 or > 790.2
total sample mean = 84.4 (994 zeros)
************************************************
spacing=8, using 2772 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2772, passno 0, spacing 8
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=25.1
skull bounding box = (61, 67, 54) --> (194, 197, 206)
using (105, 110, 130) as brain centroid...
mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find MRI
wm
before smoothing, mri peak at 109
after smoothing, mri peak at 109, scaling input intensities by 0.982
scaling channel 0 by 0.981651
initial log_p = -4.3
************************************************
First Search limited to translation only.
************************************************
max log p = -4.046112 @ (-9.091, -9.091, -27.273)
max log p = -3.926434 @ (4.545, -4.545, 4.545)
max log p = -3.926434 @ (0.000, 0.000, 0.000)
max log p = -3.911584 @ (3.409, -1.136, -5.682)
max log p = -3.897925 @ (-2.841, 2.841, 5.114)
max log p = -3.897925 @ (0.000, 0.000, 0.000)
Found translation: (-4.0, -11.9, -23.3): log p = -3.898
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9
(thresh=-3.9)
1.064 0.000 0.000 -12.315;
0.000 1.148 0.453 -81.971;
0.000 -0.432 0.988 42.250;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5
(thresh=-3.5)
1.055 -0.150 -0.059 15.090;
0.128 1.052 0.415 -82.117;
0.000 -0.464 1.062 37.519;
0.000 0.000 0.000 1.000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5
(thresh=-3.5)
1.081 -0.059 0.014 -8.838;
0.025 1.116 0.400 -76.717;
-0.035 -0.415 1.056 32.599;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3
(thresh=-3.3)
1.101 -0.061 0.014 -11.382;
0.025 1.116 0.400 -78.592;
-0.034 -0.407 1.036 33.963;
0.000 0.000 0.000 1.000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3
(thresh=-3.3)
1.098 -0.079 0.007 -7.337;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3
(thresh=-3.3)
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3
(thresh=-3.3)
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2772 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.10052 -0.07872 0.00715 -7.65093;
0.04280 1.10969 0.41752 -81.72749;
-0.03428 -0.42408 1.02550 37.91086;
0.00000 0.00000 0.00000 1.00000;
nsamples 2772
Quasinewton: input matrix
1.10052 -0.07872 0.00715 -7.65093;
0.04280 1.10969 0.41752 -81.72749;
-0.03428 -0.42408 1.02550 37.91086;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =
-0.0 tol 0.000010
Resulting transform:
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -3.3 (old=-4.3)
transform before final EM align:
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 312841 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.10052 -0.07872 0.00715 -7.65093;
0.04280 1.10969 0.41752 -81.72749;
-0.03428 -0.42408 1.02550 37.91086;
0.00000 0.00000 0.00000 1.00000;
nsamples 312841
Quasinewton: input matrix
1.10052 -0.07872 0.00715 -7.65093;
0.04280 1.10969 0.41752 -81.72749;
-0.03428 -0.42408 1.02550 37.91086;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =
3.9 tol 0.000000
final transform:
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta...
registration took 56 minutes and 24 seconds.
#--------------------------------------
#@# CA Normalize Mon Jun 24 00:59:34 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz
/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from
'/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=25.1
skull bounding box = (61, 67, 54) --> (194, 197, 206)
using (105, 110, 130) as brain centroid...
mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find MRI
wm
before smoothing, mri peak at 109
after smoothing, mri peak at 109, scaling input intensities by 0.982
scaling channel 0 by 0.981651
using 244171 sample points...
INFO: compute sample coordinates transform
1.101 -0.079 0.007 -7.651;
0.043 1.110 0.418 -81.727;
-0.034 -0.424 1.025 37.911;
0.000 0.000 0.000 1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (129, 73, 57) --> (191, 176, 203)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0
0 of 209 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 73, 57) --> (130, 171, 203)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0
0 of 240 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 151, 89) --> (179, 188, 135)
Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 230.0
1 of 12 (8.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (92, 151, 85) --> (133, 189, 136)
Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 230.0
0 of 15 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (117, 139, 115) --> (147, 197, 144)
Brain_Stem: limiting intensities to 90.0 --> 230.0
0 of 9 (0.0%) samples deleted
using 485 total control points for intensity normalization...
bias field = 1.019 +- 0.065
1 of 484 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (129, 73, 57) --> (191, 176, 203)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0
0 of 250 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 73, 57) --> (130, 171, 203)
Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0
0 of 268 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 151, 89) --> (179, 188, 135)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 233.0
0 of 60 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (92, 151, 85) --> (133, 189, 136)
Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 233.0
0 of 62 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (117, 139, 115) --> (147, 197, 144)
Brain_Stem: limiting intensities to 75.0 --> 233.0
0 of 79 (0.0%) samples deleted
using 719 total control points for intensity normalization...
bias field = 1.010 +- 0.067
0 of 719 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (129, 73, 57) --> (191, 176, 203)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 238.0
0 of 301 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 73, 57) --> (130, 171, 203)
Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 238.0
0 of 377 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 151, 89) --> (179, 188, 135)
Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0
0 of 82 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (92, 151, 85) --> (133, 189, 136)
Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0
0 of 65 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (117, 139, 115) --> (147, 197, 144)
Brain_Stem: limiting intensities to 73.0 --> 238.0
0 of 147 (0.0%) samples deleted
using 972 total control points for intensity normalization...
bias field = 1.007 +- 0.053
2 of 972 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 55 seconds.
#--------------------------------------
#@# CA Reg Mon Jun 24 01:02:30 PDT 2013
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after
-mask brainmask.mgz norm.mgz
/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.m3z
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
======= NUMBER OF OPENMP THREADS = 50 =======
reading input volume 'norm.mgz'...
reading GCA
'/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.45 (predicted orig area = 5.5)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.806, neg=0, invalid=96777
0001: dt=129.472000, rms=0.728 (9.599%), neg=0, invalid=96777
0002: dt=92.480000, rms=0.712 (2.226%), neg=0, invalid=96777
0003: dt=129.472000, rms=0.699 (1.800%), neg=0, invalid=96777
0004: dt=129.472000, rms=0.693 (0.860%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.687 (0.887%), neg=0, invalid=96777
0006: dt=129.472000, rms=0.684 (0.413%), neg=0, invalid=96777
0007: dt=129.472000, rms=0.680 (0.585%), neg=0, invalid=96777
0008: dt=110.976000, rms=0.679 (0.242%), neg=0, invalid=96777
0009: dt=110.976000, rms=0.676 (0.391%), neg=0, invalid=96777
0010: dt=110.976000, rms=0.673 (0.464%), neg=0, invalid=96777
0011: dt=110.976000, rms=0.669 (0.563%), neg=0, invalid=96777
0012: dt=110.976000, rms=0.666 (0.489%), neg=0, invalid=96777
0013: dt=110.976000, rms=0.661 (0.684%), neg=0, invalid=96777
0014: dt=110.976000, rms=0.658 (0.493%), neg=0, invalid=96777
0015: dt=110.976000, rms=0.655 (0.439%), neg=0, invalid=96777
0016: dt=110.976000, rms=0.653 (0.321%), neg=0, invalid=96777
0017: dt=110.976000, rms=0.651 (0.311%), neg=0, invalid=96777
0018: dt=110.976000, rms=0.649 (0.263%), neg=0, invalid=96777
0019: dt=110.976000, rms=0.648 (0.202%), neg=0, invalid=96777
0020: dt=110.976000, rms=0.647 (0.218%), neg=0, invalid=96777
0021: dt=110.976000, rms=0.646 (0.148%), neg=0, invalid=96777
0022: dt=110.976000, rms=0.644 (0.166%), neg=0, invalid=96777
0023: dt=110.976000, rms=0.644 (0.139%), neg=0, invalid=96777
0024: dt=110.976000, rms=0.642 (0.173%), neg=0, invalid=96777
0025: dt=110.976000, rms=0.641 (0.153%), neg=0, invalid=96777
0026: dt=110.976000, rms=0.640 (0.164%), neg=0, invalid=96777
0027: dt=110.976000, rms=0.640 (0.146%), neg=0, invalid=96777
0028: dt=110.976000, rms=0.639 (0.135%), neg=0, invalid=96777
0029: dt=110.976000, rms=0.638 (0.119%), neg=0, invalid=96777
0030: dt=110.976000, rms=0.637 (0.137%), neg=0, invalid=96777
0031: dt=110.976000, rms=0.636 (0.126%), neg=0, invalid=96777
0032: dt=110.976000, rms=0.636 (0.090%), neg=0, invalid=96777
0033: dt=110.976000, rms=0.635 (0.063%), neg=0, invalid=96777
0034: dt=129.472000, rms=0.635 (0.051%), neg=0, invalid=96777
0035: dt=129.472000, rms=0.635 (0.000%), neg=0, invalid=96777
0036: dt=129.472000, rms=0.635 (0.030%), neg=0, invalid=96777
0037: dt=129.472000, rms=0.634 (0.062%), neg=0, invalid=96777
0038: dt=129.472000, rms=0.634 (0.034%), neg=0, invalid=96777
0039: dt=129.472000, rms=0.634 (0.027%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.634, neg=0, invalid=96777
0040: dt=295.936000, rms=0.632 (0.322%), neg=0, invalid=96777