Hi,
I'm running freesurfer-Linux-centos4_x86_64-dev20060210 on Mandriva
Linux distribution, and I've had problems with some of my data.
One exits with the following error message: (log file attached)
ERROR: mri_ca_register with non-zero status
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD
Athlon(tm
) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
recon-all exited with ERRORS at Sat Feb 25 10:29:42 CET 2006
I've also had problems with the SubCort seg (log file attached),
while other data works just fine.
I'm not sure how I should fix these problems. Suggestions?
Thanks,
Martin Ystad
Medical Student
University of Bergen
Institute of Biomedicine
Jonas Lies vei 91, 5009
Bergen, Norway.
Fri Feb 24 16:45:56 CET 2006
/usr/local/freesurfer/subjects/fs517
/usr/local/freesurfer/bin//recon-all
-autorecon1 -s fs517
subjid fs517
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 1000000 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16375
########################################
program versions used
$Id: recon-all,v 1.8 2006/02/06 20:44:38 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_convert.c,v 1.119 2006/01/25 21:46:41 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
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: 06/02/24-15:45:56-GMT CVS: $Id: mri_normalize.c,v 1.44 2006/01/22 03:44:04 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_watershed.cpp,v 1.47 2006/01/15 22:39:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_segment.c,v 1.28 2006/02/06 20:37:32 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_fill.c,v 1.100 2006/01/18 20:01:50 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_tessellate.c,v 1.27 2006/01/30 13:27:37 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_inflate.c,v 1.30 2005/12/15 19:18:19 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_make_surfaces.c,v 1.68 2006/01/23 18:04:53 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_ca_register.c,v 1.45 2006/02/09 16:09:34 xhan Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:45:56-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB40_talairach_2005_12_30.gca
GCASkull RB40_talairach_with_skull_2005_12_30.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
#--------------------------------------------
#@# MotionCor Fri Feb 24 16:45:56 CET 2006
Found 2 runs
/usr/local/freesurfer/subjects/fs517/mri/orig/001.mgz
/usr/local/freesurfer/subjects/fs517/mri/orig/002.mgz
/usr/local/freesurfer/subjects/fs517
mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/fs517/mri/orig/001.mgz /usr/local/freesurfer/subjects/fs517/mri/orig/002.mgz
tmpdir is /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232
--------------------------------------------------------------
mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz.mri_motion_correct.fsl.log
--------------------------------------------------------------
-----------------------------------------
Converting /usr/local/freesurfer/subjects/fs517/mri/orig/001.mgz
Fri Feb 24 16:46:02 CET 2006
/usr/local/freesurfer/subjects/fs517
mri_convert /usr/local/freesurfer/subjects/fs517/mri/orig/001.mgz /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.img -odt float
reading from /usr/local/freesurfer/subjects/fs517/mri/orig/001.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.img...
Analyze Output Matrix
0.000 0.000 1.400 -89.468;
-0.938 0.000 0.000 151.377;
0.000 -0.938 0.000 132.352;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /usr/local/freesurfer/subjects/fs517/mri/orig/002.mgz
Fri Feb 24 16:46:04 CET 2006
/usr/local/freesurfer/subjects/fs517
mri_convert /usr/local/freesurfer/subjects/fs517/mri/orig/002.mgz /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img -odt float
reading from /usr/local/freesurfer/subjects/fs517/mri/orig/002.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img...
Analyze Output Matrix
0.000 0.000 1.400 -89.468;
-0.938 0.000 0.000 151.377;
0.000 -0.938 0.000 132.352;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img
Fri Feb 24 16:46:06 CET 2006
/usr/local/freesurfer/subjects/fs517
fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.img -i /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img -o /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.img -tmpdir /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232 -cleanup
\n\n
$Id: fsl_rigid_register,v 1.13 2006/01/24 19:51:34 greve Exp $
Fri Feb 24 16:46:06 CET 2006
/usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.img
Reference is analyze, not converting
Input is analyze, not converting
Output is analyze, not converting
--------------------------------------
/usr/local/freesurfer/subjects/fs517
calling eval flirt -in /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.hdr -out /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.hdr -omat /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.fslmat
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
Started at Fri Feb 24 16:46:06 CET 2006
Ended at Fri Feb 24 16:53:24 CET 2006
fsl_rigid_register Done
To check results, run:
tkmedit -f /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.img -aux /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.img
mv /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/resampled.img /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img
-----------------------------------------
Averaging
Fri Feb 24 16:53:25 CET 2006
/usr/local/freesurfer/subjects/fs517
inhibiting isotropic volume interpolation
1 of 2: reading /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-1.img...
2 of 2: reading /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/cor-2.img...
writing to /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/avgvol.img...
alignment and averaging took 0 minutes and 15 seconds.
INFO: analyzeRead(): min = 0, max = 2038
INFO: analyzeRead(): min = 0, max = 1675
Analyze Output Matrix
0.000 0.000 1.400 -89.468;
-0.938 0.000 0.000 151.377;
0.000 -0.938 0.000 132.352;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting Average to output
Fri Feb 24 16:53:41 CET 2006
/usr/local/freesurfer/subjects/fs517
mri_convert /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/avgvol.img /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz -tr 9.452 -te 2.212 -TI 450 -flip_angle 0.122173
mri_convert /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/avgvol.img /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz -tr 9.452 -te 2.212 -TI 450 -flip_angle 0.122173
reading from /usr/local/freesurfer/subjects/fs517/mri/tmp-mri_motion_correct.fsl-29232/avgvol.img...
INFO: analyzeRead(): min = 0, max = 1774.5
TR=9.45, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz...
-----------------------------------------
Started at: Fri Feb 24 16:45:57 CET 2006
Ended at: Fri Feb 24 16:53:55 CET 2006
mri_motion_correct.fsl: done
/usr/local/freesurfer/subjects/fs517
mri_convert /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz /usr/local/freesurfer/subjects/fs517/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz /usr/local/freesurfer/subjects/fs517/mri/orig.mgz --conform
reading from /usr/local/freesurfer/subjects/fs517/mri/rawavg.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
Original Data has (0.9375, 0.9375, 1.4) mm size and (256, 256, 124) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 3 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/fs517/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/fs517/mri/orig.mgz /usr/local/freesurfer/subjects/fs517/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Fri Feb 24 16:54:28 CET 2006
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/fs517/mri
/usr/local/freesurfer/bin//mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
Fri Feb 24 16:54:29 CET 2006
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
tmpdir is ./tmp.mri_nu_correct.mni.30041
/usr/local/freesurfer/subjects/fs517/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30041/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30041/nu0.mnc
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from orig.mgz...
Talairach transform /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm ...which does not exist
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to ./tmp.mri_nu_correct.mni.30041/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Feb 24 16:54:44 CET 2006
nu_correct -clobber ./tmp.mri_nu_correct.mni.30041/nu0.mnc ./tmp.mri_nu_correct.mni.30041/nu1.mnc
[martin@localhost:/usr/local/freesurfer/subjects/fs517/mri/] [2006-02-24 16:54:45] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /home/martin/tmp/nu_correct_30090/ ./tmp.mri_nu_correct.mni.30041/nu0.mnc ./tmp.mri_nu_correct.mni.30041/nu1.imp
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 3
CV of field change: 0.000696711
[martin@localhost:/usr/local/freesurfer/subjects/fs517/mri/] [2006-02-24 16:54:54] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30041/nu0.mnc /home/martin/tmp/nu_correct_30090//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
--------------------------------------------------------
Iteration 2 Fri Feb 24 16:55:05 CET 2006
nu_correct -clobber ./tmp.mri_nu_correct.mni.30041/nu1.mnc ./tmp.mri_nu_correct.mni.30041/nu2.mnc
[martin@localhost:/usr/local/freesurfer/subjects/fs517/mri/] [2006-02-24 16:55:05] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /home/martin/tmp/nu_correct_30191/ ./tmp.mri_nu_correct.mni.30041/nu1.mnc ./tmp.mri_nu_correct.mni.30041/nu2.imp
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 2
CV of field change: 0.000855481
[martin@localhost:/usr/local/freesurfer/subjects/fs517/mri/] [2006-02-24 16:55:14] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30041/nu1.mnc /home/martin/tmp/nu_correct_30191//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
mri_convert ./tmp.mri_nu_correct.mni.30041/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.30041/nu2.mnc nu.mgz --like orig.mgz
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from ./tmp.mri_nu_correct.mni.30041/nu2.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
Talairach transform /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm ...which does not exist
writing to nu.mgz...
Fri Feb 24 16:55:51 CET 2006
mri_nu_correct.mni done
#--------------------------------------------
#@# Talairach Fri Feb 24 16:55:51 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/usr/local/freesurfer/subjects/fs517/mri
/usr/local/freesurfer/bin//talairach
--i nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
Fri Feb 24 16:55:52 CET 2006
tmpdir is transforms/tmp.talairach.30326
/usr/local/freesurfer/subjects/fs517/mri
mri_convert nu.mgz transforms/tmp.talairach.30326/src.mnc
mri_convert nu.mgz transforms/tmp.talairach.30326/src.mnc
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from nu.mgz...
Talairach transform /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs517/mri/transforms/talairach.xfm ...which does not exist
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.30326/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30326/src.mnc transforms/talairach.auto.xfm
Fri Feb 24 16:57:07 CET 2006
talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Intensity Normalization Fri Feb 24 16:57:08 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
1.014 -0.033 0.014 4.306;
0.030 0.971 0.144 -50.364;
-0.019 -0.149 1.009 -34.447;
0.000 0.000 0.000 1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to T1.mgz
3D bias adjustment took 12 minutes and 45 seconds.
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
#--------------------------------------------
#@# Skull Stripping Fri Feb 24 17:09:58 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_watershed -atlas T1.mgz brainmask.auto.mgz
Mode: Atlas analysis
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C
*************************WATERSHED**************************
preflooding height equal to 25 percent
Sorting...
T1-weighted MRI image
modification of the preflooding height to 15 percent
Count how many 110 voxels are present : 112839
Find the largest 110-component...
heap usage = 185668 Kbytes.
removing small segments (less than 1 percent of maxarea).done
And identify it as the main brain basin...done
Main component: 92728 voxels
first estimation of the COG coord: x=131 y=92 z=123 r=101
first estimation of the main basin volume: 4371424 voxels
global maximum in x=108, y=66, z=94, Imax=255
CSF=21, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
done
Analyze
main basin size= 1495116 voxels, voxel volume =1.000
= 1495116 mmm3 = 1495.116 cm3
done
PostAnalyze...
ambiguous basin, merged: at least 31 ambiguous voxels; size: 27626 voxels
***** 1 basin(s) merged in 2 iteration(s)
***** 27626 voxel(s) added to the main basin
done
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=94, z=121, r=9868 iterations
Problem with the least square interpolation in GM_MIN calculation.
before analyzing : CSF_MAX=48, TRANSITION=36, GM_MIN=24, GM=53
after analyzing : CSF_MAX=31, TRANSITION=36, GM_MIN=36, GM=40
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...77 iterations
*********************VALIDATION*********************
Rigid alignment...
scanning 32.00 degree nbhd, min sse = 4.23 at ( 0.00, 0.00, 8.00)
scanning 16.00 degree nbhd, min sse = 4.19 at ( 4.00, 0.00, 0.00)
scanning 8.00 degree nbhd, min sse = 4.18 at (-2.00, 0.00, 0.00)
scanning 4.00 degree nbhd, min sse = 4.15 at ( 1.00, 1.00, -1.00)
done
before rotation: sse = 5.38, sigma = 12.07
after rotation: sse = 4.15, sigma = 8.32
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 5.17, its var is 14.22
before Erosion-Dilatation 5.21% of inacurate vertices
after Erosion-Dilatation 5.45% of inacurate vertices
32.62% of 'positive' inacurate vertices
67.38% of 'negative' inacurate vertices
THE SEGMENTATION IS PROBABLY NOT CORRECT
Scaling of atlas fields onto current surface fields
Correcting the shape of the surface...38 iterations
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...
mri_strip_skull: done peeling brainComputing COG for corrected surface
Initial Configuration: NRG=36117.778000, ( -1.648721 , 23.857458 , 45.922814 )
Final Minimum found: NRG=35606.395456, ( -2.206277 , 23.926185 , 45.779192 )done
The shape of the surface was incorrect,
hence we rigidly realign the surface with the template
Rigid alignment...
scanning 32.00 degree nbhd, min sse = 0.77 at ( 0.00, 0.00, 8.00)
scanning 16.00 degree nbhd, min sse = 0.74 at ( 4.00, 0.00, 0.00)
scanning 8.00 degree nbhd, min sse = 0.59 at (-2.00, 0.00, -2.00)
scanning 4.00 degree nbhd, min sse = 0.59 at ( 0.00, 0.00, 0.00)
done
before rotation: sse = 1.59, sigma = 2.49
after rotation: sse = 0.59, sigma = 1.14
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 0.59, its var is 0.86
before Erosion-Dilatation 0.01% of inacurate vertices
after Erosion-Dilatation 0.00% of inacurate vertices
Validation of the shape of the surface done.67 iterations
mri_strip_skull: done peeling brain
Brain Size = 1598299 voxels, voxel volume = 1.000 mm3
= 1598299 mmm3 = 1598.299 cm3
******************************
Save...done
INFO: Fixing vertex area
cp brainmask.auto.mgz brainmask.mgz
#------------------------------------------
recon-all finished without error at Fri Feb 24 17:26:47 CET 2006
New invocation of recon-all
Fri Feb 24 17:41:27 CET 2006
/usr/local/freesurfer/subjects/fs517
/usr/local/freesurfer/bin//recon-all
-skullstrip -wsthresh 35 -s fs517
subjid fs517
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 1000000 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16375
########################################
program versions used
$Id: recon-all,v 1.8 2006/02/06 20:44:38 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:27-GMT CVS: $Id: mri_convert.c,v 1.119 2006/01/25 21:46:41 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
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: 06/02/24-16:41:27-GMT CVS: $Id: mri_normalize.c,v 1.44 2006/01/22 03:44:04 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:27-GMT CVS: $Id: mri_watershed.cpp,v 1.47 2006/01/15 22:39:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:27-GMT CVS: $Id: mri_segment.c,v 1.28 2006/02/06 20:37:32 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_fill.c,v 1.100 2006/01/18 20:01:50 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_tessellate.c,v 1.27 2006/01/30 13:27:37 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_inflate.c,v 1.30 2005/12/15 19:18:19 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_make_surfaces.c,v 1.68 2006/01/23 18:04:53 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_ca_register.c,v 1.45 2006/02/09 16:09:34 xhan Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:41:28-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB40_talairach_2005_12_30.gca
GCASkull RB40_talairach_with_skull_2005_12_30.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
#--------------------------------------------
#@# Skull Stripping Fri Feb 24 17:41:28 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -atlas -h 35 T1.mgz brainmask.auto.mgz
Mode: Atlas analysis
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C
*************************WATERSHED**************************
preflooding height equal to 35 percent
Sorting...
T1-weighted MRI image
Count how many 110 voxels are present : 112839
Find the largest 110-component...
heap usage = 219548 Kbytes.
removing small segments (less than 1 percent of maxarea).done
And identify it as the main brain basin...done
Main component: 92728 voxels
first estimation of the COG coord: x=131 y=92 z=123 r=101
first estimation of the main basin volume: 4371424 voxels
global maximum in x=108, y=66, z=94, Imax=255
CSF=21, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
done
Analyze
main basin size= 1697069 voxels, voxel volume =1.000
= 1697069 mmm3 = 1697.069 cm3
done
PostAnalyze...
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=130,y=97, z=121, r=12584 iterations
Problem with the least square interpolation in GM_MIN calculation.
before analyzing : CSF_MAX=49, TRANSITION=36, GM_MIN=26, GM=53
after analyzing : CSF_MAX=31, TRANSITION=36, GM_MIN=36, GM=40
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...75 iterations
*********************VALIDATION*********************
Rigid alignment...
scanning 32.00 degree nbhd, min sse = 3.49 at ( 0.00, 0.00, 0.00)
scanning 16.00 degree nbhd, min sse = 3.03 at ( 0.00, -4.00, 4.00)
scanning 8.00 degree nbhd, min sse = 3.00 at ( 0.00, 2.00, 0.00)
scanning 4.00 degree nbhd, min sse = 2.99 at ( 0.00, -1.00, 0.00)
done
before rotation: sse = 3.49, sigma = 4.89
after rotation: sse = 2.99, sigma = 4.20
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 3.14, its var is 3.71
before Erosion-Dilatation 1.22% of inacurate vertices
after Erosion-Dilatation 0.00% 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...39 iterations
mri_strip_skull: done peeling brain
Brain Size = 1592231 voxels, voxel volume = 1.000 mm3
= 1592231 mmm3 = 1592.231 cm3
******************************
Save...done
Keeping brain edits brainmask.auto.mgz brainmask.mgz
INFO: Fixing vertex area
Keeping edits ...
Saving kept edits to brainmask.mgz .....
#------------------------------------------
recon-all finished without error at Fri Feb 24 17:45:21 CET 2006
New invocation of recon-all
Fri Feb 24 17:58:37 CET 2006
/usr/local/freesurfer/subjects/fs517
/usr/local/freesurfer/bin//recon-all
-autorecon2 -s fs517
subjid fs517
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 1000000 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16375
########################################
program versions used
$Id: recon-all,v 1.8 2006/02/06 20:44:38 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_convert.c,v 1.119 2006/01/25 21:46:41 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
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: 06/02/24-16:58:37-GMT CVS: $Id: mri_normalize.c,v 1.44 2006/01/22 03:44:04 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_watershed.cpp,v 1.47 2006/01/15 22:39:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_segment.c,v 1.28 2006/02/06 20:37:32 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_fill.c,v 1.100 2006/01/18 20:01:50 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_tessellate.c,v 1.27 2006/01/30 13:27:37 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_inflate.c,v 1.30 2005/12/15 19:18:19 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.68 2006/01/23 18:04:53 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_ca_register.c,v 1.45 2006/02/09 16:09:34 xhan Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB40_talairach_2005_12_30.gca
GCASkull RB40_talairach_with_skull_2005_12_30.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
#-------------------------------------
#@# EM Registration Fri Feb 24 17:58:37 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
average std = 7.0 using min determinant for regularization = 4.9
0 singular and 1794 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
total sample mean = 85.3 (517 zeros)
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2400, passno 0, spacing 8
************************************************
First Search limited to translation only.
************************************************
Found translation: (-5.1, 23.3, -19.9): log p = -36786.6
Result so far: scale 1.000: max_log_p=-33584.8, old_max_log_p =-36786.6 (thresh=-36749.9)
1.062 0.000 0.000 -13.302;
0.000 1.125 0.000 11.388;
0.000 0.000 1.000 -19.886;
0.000 0.000 0.000 1.000;
Result so far: scale 1.000: max_log_p=-33584.8, old_max_log_p =-33584.8 (thresh=-33551.3)
1.062 0.000 0.000 -13.302;
0.000 1.125 0.000 11.388;
0.000 0.000 1.000 -19.886;
0.000 0.000 0.000 1.000;
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.06250 0.00000 0.00000 -13.30235;
0.00000 1.12500 0.00000 11.38752;
0.00000 0.00000 1.00000 -19.88637;
0.00000 0.00000 0.00000 1.00000;
nsamples 2400
Quasinewton: input matrix
1.06250 0.00000 0.00000 -13.30235;
0.00000 1.12500 0.00000 11.38752;
0.00000 0.00000 1.00000 -19.88637;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
fp = 33031.250000, fret = 33031.250000, ftol = 0.000010, EPS = 0.000000
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.06250 0.00000 0.00000 -13.30235;
0.00000 1.12500 0.00000 11.38752;
0.00000 0.00000 1.00000 -19.88637;
0.00000 0.00000 0.00000 1.00000;
nsamples 250643
Quasinewton: input matrix
1.06250 0.00000 0.00000 -13.30235;
0.00000 1.12500 0.00000 11.38752;
0.00000 0.00000 1.00000 -19.88637;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
freeing gibbs priors...done.
bounding unknown intensity as < 14.7 or > 943.6
************************************************
spacing=8, using 2400 sample points, tol=1.00e-05...
************************************************
Note: program considers input volume #1 as the most T1-like
using real data threshold=27.0
using (107, 73, 128) as brain centroid...
mean wm in atlas = 106, using box (90,60,107) --> (123, 86,148) to find MRI wm
before smoothing, mri peak at 73
after smoothing, mri peak at 73, scaling input intensities by 1.458
scaling channel 0 by 1.45759
initial log_p = -114449.7
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
reducing scale to 0.2500
***********************************************
Computing MAP estimate using 2400 samples...
***********************************************
dfp_em_step_func: 002: -log(p) = 33584.8
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.12, 0.00, 11.39)
( 0.00, 0.00, 1.00, -19.89)
dfp_em_step_func: 003: -log(p) = 33480.0
after pass:transform: ( 1.06, -0.00, -0.00, -13.30)
( 0.00, 1.12, 0.00, 11.39)
( 0.00, 0.00, 1.00, -19.89)
dfp_em_step_func: 004: -log(p) = 33087.9
after pass:transform: ( 1.06, -0.00, 0.00, -13.30)
( -0.01, 1.12, 0.00, 11.39)
( 0.00, 0.00, 1.00, -19.89)
dfp_em_step_func: 005: -log(p) = 33031.2
after pass:transform: ( 1.06, -0.00, 0.00, -13.30)
( -0.01, 1.12, 0.00, 11.39)
( 0.00, 0.00, 1.00, -19.89)
outof QuasiNewtonEMA: 007: -log(p) = 33031.2 tol 0.000010
Resulting transform:
1.062 0.000 0.000 -13.302;
0.000 1.125 0.000 11.388;
0.000 0.000 1.000 -19.886;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -33584.8 (old=-114449.7)
transform before final EM align:
1.062 0.000 0.000 -13.302;
0.000 1.125 0.000 11.388;
0.000 0.000 1.000 -19.886;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 250643 samples.
**************************************************
dfp_em_step_func: 006: -log(p) = 3802466.0
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.12, 0.00, 11.39)
( 0.00, 0.00, 1.00, -19.89)
dfp_em_step_func: 007: -log(p) = 3787240.5
after pass:transform: ( 1.07, 0.01, 0.01, -13.30)
( 0.01, 1.13, 0.02, 11.39)
( 0.01, 0.01, 1.01, -19.89)
dfp_em_step_func: 008: -log(p) = 3623666.2
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.12, 0.01, 11.39)
( 0.00, 0.01, 1.01, -19.89)
dfp_em_step_func: 009: -log(p) = 3590374.8
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.12, 0.01, 11.39)
( 0.00, 0.01, 1.01, -19.89)
dfp_em_step_func: 010: -log(p) = 3572787.0
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.13, 0.01, 11.39)
( 0.00, 0.01, 1.01, -19.89)
dfp_em_step_func: 011: -log(p) = 3561006.5
after pass:transform: ( 1.06, 0.00, 0.00, -13.30)
( 0.00, 1.13, 0.01, 11.39)
( 0.01, 0.01, 1.01, -19.89)
outof QuasiNewtonEMA: 013: -log(p) = 3553376.2 tol 0.000000
final transform:
1.061 0.002 0.005 -13.302;
0.004 1.125 0.013 11.388;
0.006 0.008 1.010 -19.886;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta...
registration took 13 minutes and 39 seconds.
#--------------------------------------
#@# CA Normalize Fri Feb 24 18:12:16 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.lta norm.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
reading transform from 'transforms/talairach.lta'...
INFO: compute sample coordinates transform
1.061 0.002 0.005 -13.302;
0.004 1.125 0.013 11.388;
0.006 0.008 1.010 -19.886;
0.000 0.000 0.000 1.000;
INFO: transform used
reading input volume from nu.mgz...
Note: program considers input volume #1 as the most T1-like
using real data threshold=27.0
using (107, 73, 128) as brain centroid...
mean wm in atlas = 106, using box (90,60,107) --> (123, 86,148) to find MRI wm
before smoothing, mri peak at 73
after smoothing, mri peak at 73, scaling input intensities by 1.458
scaling channel 0 by 1.45759
using 250643 sample points...
finding control points in Left_Cerebral_White_Matter....
found 42041 control points for structure...
bounding box (130, 36, 38) --> (191, 140, 208)
Left_Cerebral_White_Matter: limiting intensities to 140.0 --> 164.0
137 of 166 (82.5%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 41886 control points for structure...
bounding box (66, 36, 40) --> (131, 139, 212)
Right_Cerebral_White_Matter: limiting intensities to 144.0 --> 154.0
170 of 178 (95.5%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 2779 control points for structure...
bounding box (131, 109, 63) --> (168, 147, 121)
Left_Cerebellum_White_Matter: limiting intensities to 111.0 --> 130.0
12 of 39 (30.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2673 control points for structure...
bounding box (89, 111, 63) --> (129, 147, 121)
Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 121.0
18 of 49 (36.7%) samples deleted
finding control points in Brain_Stem....
found 3627 control points for structure...
bounding box (113, 104, 99) --> (146, 162, 135)
Brain_Stem: limiting intensities to 96.0 --> 105.0
65 of 96 (67.7%) samples deleted
using 528 total control points for intensity normalization...
bias field = 0.749 +- 0.066
0 of 126 control points discarded
writing normalized volume to norm.mgz...
freeing GCA...done.
normalization took 3 minutes and 4 seconds.
#--------------------------------------
#@# CA Reg Fri Feb 24 18:15:21 CET 2006
/usr/local/freesurfer/subjects/fs517/mri
mri_ca_register -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.m3z
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
renormalizing by structure alignment....
renormalizing input #0
aligning Right_Cerebral_White_Matter...
source mean =71.6458, std = 17.656
X:64-135; Y:33-143; Z:37-217
gca peak = 0.05458 (115)
mri peak = 0.04321 (84)
Right_Cerebral_White_Matter (41): linear fit = 0.77 x + 0.0 (90059 voxels, overlap=0.085)
aligning Left_Cerebral_White_Matter...
source mean =71.4426, std = 17.2837
X:128-195; Y:34-145; Z:35-213
gca peak = 0.05666 (115)
mri peak = 0.03281 (89)
Left_Cerebral_White_Matter (2): linear fit = 0.80 x + 0.0 (143906 voxels, overlap=0.066)
aligning Right_Hippocampus...
source mean =67.5789, std = 14.8059
X:91-127; Y:97-132; Z:100-148
gca peak = 0.11828 (64)
mri peak = 0.03242 (42)
overlap = 4.06559e-06, overlap_threshold = 0.001
insufficient overlap 0.0000 in histograms - rejecting
aligning Left_Hippocampus...
source mean =68.971, std = 15.2905
X:134-170; Y:98-132; Z:100-148
gca peak = 0.16548 (65)
mri peak = 0.04956 (46)
overlap = 0.000319885, overlap_threshold = 0.001
insufficient overlap 0.0003 in histograms - rejecting
aligning Left_Cerebral_Cortex...
gca peak = 0.05861 (67)
mri peak = 0.01989 (24)
uniform distribution in MR - rejecting arbitrary fit
aligning Right_Cerebral_Cortex...
gca peak = 0.06315 (69)
mri peak = 0.01646 (39)
uniform distribution in MR - rejecting arbitrary fit
aligning Left_Lateral_Ventricle...
source mean =60.8841, std = 27.4529
X:128-167; Y:76-113; Z:69-173
gca peak = 0.05355 (17)
mri peak = 0.15838 (13)
Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (7016 voxels, overlap=0.195)
aligning Right_Lateral_Ventricle...
source mean =59.1704, std = 26.9301
X:96-133; Y:76-113; Z:65-175
gca peak = 0.06083 (18)
mri peak = 0.11711 (13)
Right_Lateral_Ventricle (43): linear fit = 0.70 x + 0.0 (6083 voxels, overlap=0.171)
aligning Right_Caudate...
source mean =69.7558, std = 26.6068
X:108-130; Y:77-112; Z:118-172
gca peak = 0.10620 (72)
mri peak = 0.05531 (49)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (762 voxels, overlap=0.173)
aligning Left_Caudate...
source mean =69.3229, std = 29.8702
X:133-155; Y:77-112; Z:116-170
gca peak = 0.11131 (84)
mri peak = 0.03805 (54)
Left_Caudate (11): linear fit = 0.68 x + 0.0 (636 voxels, overlap=0.054)
aligning Left_Cerebellum_Cortex...
source mean =52.4157, std = 18.6029
X:128-186; Y:100-165; Z:49-121
gca peak = 0.06541 (56)
mri peak = 0.02739 (49)
uniform distribution in MR - rejecting arbitrary fit
aligning Right_Cerebellum_Cortex...
source mean =52.1878, std = 18.598
X:77-135; Y:100-167; Z:49-122
gca peak = 0.07158 (57)
mri peak = 0.04235 (49)
Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (34023 voxels, overlap=0.368)
aligning Left_Cerebellum_White_Matter...
source mean =71.6369, std = 14.2549
X:128-173; Y:107-151; Z:61-125
gca peak = 0.07712 (87)
mri peak = 0.04506 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9536 voxels, overlap=0.251)
aligning Right_Cerebellum_White_Matter...
source mean =69.3825, std = 16.2292
X:87-133; Y:108-151; Z:61-125
gca peak = 0.09487 (84)
mri peak = 0.05563 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.15 x + 0.0 (4980 voxels, overlap=0.442)
aligning Left_Amygdala...
source mean =64.0185, std = 14.0566
X:134-164; Y:110-133; Z:133-154
gca peak = 0.11798 (62)
mri peak = 0.05208 (130)
overlap = 0, overlap_threshold = 0.001
insufficient overlap 0.0000 in histograms - rejecting
aligning Right_Amygdala...
source mean =63.4016, std = 12.922
X:97-124; Y:110-133; Z:133-154
invalid transform detected (det=0.2395
gca peak = 0.15512 (63)
mri peak = 0.10194 (47)
Right_Amygdala (54): linear fit = 0.75 x + 0.0 (748 voxels, overlap=0.003)
aligning Left_Thalamus_Proper...
source mean =78.1722, std = 25.911
X:128-158; Y:85-113; Z:105-149
gca peak = 0.06295 (104)
mri peak = 0.03066 (71)
Left_Thalamus_Proper (10): linear fit = 0.77 x + 0.0 (7982 voxels, overlap=0.052)
aligning Right_Thalamus_Proper...
source mean =77.0952, std = 25.2253
X:105-133; Y:85-111; Z:107-149
gca peak = 0.06253 (102)
mri peak = 0.04277 (79)
Right_Thalamus_Proper (49): linear fit = 0.90 x + 0.0 (5302 voxels, overlap=0.262)
aligning Left_Putamen...
source mean =82.4018, std = 10.6882
X:136-168; Y:87-119; Z:121-168
gca peak = 0.06876 (82)
mri peak = 0.04284 (68)
Left_Putamen (12): linear fit = 0.75 x + 0.0 (4651 voxels, overlap=0.048)
aligning Right_Putamen...
source mean =82.3447, std = 10.441
X:93-124; Y:87-119; Z:122-168
gca peak = 0.06949 (87)
mri peak = 0.03911 (47)
overlap = 0.000746276, overlap_threshold = 0.001
insufficient overlap 0.0007 in histograms - rejecting
aligning Left_Pallidum...
source mean =83.9109, std = 15.6384
X:138-160; Y:94-114; Z:127-156
gca peak = 0.11762 (98)
mri peak = 0.07950 (105)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (354 voxels, overlap=0.565)
aligning Right_Pallidum...
source mean =90.5484, std = 10.0122
X:102-124; Y:94-114; Z:128-156
gca peak = 0.16855 (106)
mri peak = 0.09043 (91)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (292 voxels, overlap=0.043)
aligning Brain_Stem...
source mean =67.8273, std = 25.9565
X:111-150; Y:101-167; Z:96-139
gca peak = 0.04887 (88)
mri peak = 0.04969 (78)
Brain_Stem (16): linear fit = 0.90 x + 0.0 (14821 voxels, overlap=0.382)
aligning Right_VentralDC...
source mean =75.4099, std = 22.8204
X:102-133; Y:101-124; Z:113-151
gca peak = 0.05769 (94)
mri peak = 0.04946 (89)
Right_VentralDC (60): linear fit = 0.93 x + 0.0 (2679 voxels, overlap=0.350)
aligning Left_VentralDC...
source mean =75.9784, std = 22.3526
X:128-159; Y:101-124; Z:112-151
gca peak = 0.05759 (95)
mri peak = 0.04297 (91)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2482 voxels, overlap=0.457)
aligning Third_Ventricle...
source mean =56.3838, std = 21.5672
X:126-137; Y:94-120; Z:113-151
gca peak = 0.14462 (29)
mri peak = 0.04267 (18)
Third_Ventricle (14): linear fit = 2.20 x + 0.0 (466 voxels, overlap=0.057)
aligning Fourth_Ventricle...
source mean =55.0988, std = 21.9018
X:119-142; Y:105-156; Z:89-122
gca peak = 0.11044 (27)
mri peak = 0.27240 (13)
Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (1312 voxels, overlap=0.207)
estimating mean gm scale to be 0.85 x + 0.0
estimating mean wm scale to be 0.79 x + 0.0
estimating mean csf scale to be 0.62 x + 0.0
writing gca to talairach.gca...
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
pct change decreased
switching integration type to fixed (done=1)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
rms increased - undoing step...
pct change < tol 0.025, nsmall = 2 of 2
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
pct change decreased
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
pct change decreased
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
rms increased - undoing step...
setting smoothness coefficient to 0.40
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 1.00
blurring input image with Gaussian with sigma=2.000...
pct change decreased
rms increased - undoing step...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=0)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
resetting metric properties...
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=1)
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
rms increased - undoing step...
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
pct change < tol 0.025, nsmall = 1 of 2
rms increased - undoing step...
pct change < tol 0.025, nsmall = 2 of 2
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 0.40
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 1.00
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
resetting metric properties...
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
writing output transformation to transforms/talairach.m3z...
registration took 985 minutes and 32 seconds.
#--------------------------------------
#@# Remove Neck Sat Feb 25 10:40:53 CET 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain
reading atlas '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
gcam->type = vox
reading labels out of gcam file...
removing structures at least 25 mm from brain...
11171311 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 4 minutes and 28 seconds.
#--------------------------------------
#@# SkullLTA Sat Feb 25 10:45:22 CET 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB40_talairach_with_skull_2005_12_30.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB40_talairach_with_skull_2005_12_30.gca'...
setting gca type = Normal gca type
average std = 23.5 using min determinant for regularization = 55.1
0 singular and 5489 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
total sample mean = 92.0 (1496 zeros)
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3583, passno 0, spacing 8
Result so far: scale 1.000: max_log_p=-19610.5, old_max_log_p =-19833.9 (thresh=-19814.0)
0.929 0.002 0.004 3.974;
0.004 1.196 0.014 4.428;
0.006 0.009 1.137 -35.566;
0.000 0.000 0.000 1.000;
Result so far: scale 1.000: max_log_p=-19610.5, old_max_log_p =-19610.5 (thresh=-19590.9)
0.929 0.002 0.004 3.974;
0.004 1.196 0.014 4.428;
0.006 0.009 1.137 -35.566;
0.000 0.000 0.000 1.000;
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
0.92880 0.00174 0.00401 3.97359;
0.00431 1.19573 0.01404 4.42848;
0.00622 0.00903 1.13670 -35.56587;
0.00000 0.00000 0.00000 1.00000;
nsamples 3583
Quasinewton: input matrix
0.92880 0.00174 0.00401 3.97359;
0.00431 1.19573 0.01404 4.42848;
0.00622 0.00903 1.13670 -35.56587;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
fp = 19252.595703, fret = 19252.595703, ftol = 0.000010, EPS = 0.000000
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
0.92880 0.00174 0.00401 3.97359;
0.00431 1.19573 0.01404 4.42848;
0.00622 0.00903 1.13670 -35.56587;
0.00000 0.00000 0.00000 1.00000;
nsamples 394897
Quasinewton: input matrix
0.92880 0.00174 0.00401 3.97359;
0.00431 1.19573 0.01404 4.42848;
0.00622 0.00903 1.13670 -35.56587;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
freeing gibbs priors...done.
bounding unknown intensity as < 20.7 or > 755.6
************************************************
spacing=8, using 3583 sample points, tol=1.00e-05...
************************************************
Note: program considers input volume #1 as the most T1-like
using real data threshold=23.0
using (103, 77, 130) as brain centroid...
mean wm in atlas = 117, using box (84,56,105) --> (122, 98,155) to find MRI wm
before smoothing, mri peak at 73
after smoothing, mri peak at 74, scaling input intensities by 1.585
scaling channel 0 by 1.58468
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
reducing scale to 0.2500
***********************************************
Computing MAP estimate using 3583 samples...
***********************************************
dfp_em_step_func: 002: -log(p) = 19610.5
after pass:transform: ( 0.93, 0.00, 0.00, 3.97)
( 0.00, 1.20, 0.01, 4.43)
( 0.01, 0.01, 1.14, -35.57)
dfp_em_step_func: 003: -log(p) = 19280.2
after pass:transform: ( 0.93, 0.00, 0.00, 3.97)
( 0.00, 1.19, 0.01, 4.43)
( 0.00, 0.01, 1.14, -35.57)
dfp_em_step_func: 004: -log(p) = 19257.0
after pass:transform: ( 0.93, 0.00, 0.00, 3.97)
( 0.00, 1.19, 0.01, 4.43)
( 0.00, 0.01, 1.13, -35.57)
dfp_em_step_func: 005: -log(p) = 19252.6
after pass:transform: ( 0.93, 0.00, 0.00, 3.97)
( 0.00, 1.19, 0.01, 4.43)
( 0.00, 0.01, 1.13, -35.57)
outof QuasiNewtonEMA: 007: -log(p) = 19252.6 tol 0.000010
Resulting transform:
0.929 0.002 0.004 3.974;
0.004 1.196 0.014 4.428;
0.006 0.009 1.137 -35.566;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -19610.5 (old=-19833.9)
transform before final EM align:
0.929 0.002 0.004 3.974;
0.004 1.196 0.014 4.428;
0.006 0.009 1.137 -35.566;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 394897 samples.
**************************************************
dfp_em_step_func: 006: -log(p) = 2617164.8
after pass:transform: ( 0.93, 0.00, 0.00, 3.97)
( 0.00, 1.20, 0.01, 4.43)
( 0.01, 0.01, 1.14, -35.57)
dfp_em_step_func: 007: -log(p) = 2587377.8
after pass:transform: ( 0.93, -0.00, -0.00, 3.97)
( -0.01, 1.19, 0.01, 4.43)
( 0.00, 0.01, 1.13, -35.57)
dfp_em_step_func: 008: -log(p) = 2586760.8
after pass:transform: ( 0.93, -0.00, -0.00, 3.97)
( -0.00, 1.19, 0.02, 4.43)
( 0.00, 0.01, 1.14, -35.57)
dfp_em_step_func: 009: -log(p) = 2577883.5
after pass:transform: ( 0.93, -0.00, -0.00, 3.97)
( -0.00, 1.19, 0.02, 4.43)
( 0.00, 0.01, 1.14, -35.57)
dfp_em_step_func: 010: -log(p) = 2558076.2
after pass:transform: ( 0.94, -0.01, -0.00, 3.97)
( -0.01, 1.18, 0.02, 4.43)
( 0.00, 0.01, 1.13, -35.57)
dfp_em_step_func: 011: -log(p) = 2558062.0
after pass:transform: ( 0.94, -0.01, -0.00, 3.97)
( -0.01, 1.18, 0.02, 4.43)
( 0.00, 0.01, 1.13, -35.57)
outof QuasiNewtonEMA: 013: -log(p) = 2558055.5 tol 0.000000
final transform:
0.935 -0.006 -0.002 3.974;
-0.009 1.183 0.019 4.428;
0.001 0.009 1.135 -35.566;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta...
registration took 16 minutes and 0 seconds.
#--------------------------------------
#@# SubCort Seg Sat Feb 25 11:01:23 CET 2006
mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca aseg.auto.mgz
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
reading 1 input volumes...
reading classifier array from /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca...
setting gca type = Normal gca type
reading input volume from norm.mgz...
average std[0] = 7.0
reading transform from transforms/talairach.m3z...
gcam->type = vox
reading labels out of gcam file...
Atlas used for the 3D morph was /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca
average std = 7.0 using min determinant for regularization = 4.9
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.07207 (113)
mri peak = 0.05029 (84)
Right_Cerebral_White_Matter (41): linear fit = 0.80 x + 0.0 (51383 voxels, overlap=0.030)
gca peak = 0.07200 (114)
mri peak = 0.04171 (88)
Left_Cerebral_White_Matter (2): linear fit = 0.80 x + 0.0 (56116 voxels, overlap=0.034)
gca peak = 0.25438 (63)
mri peak = 0.06625 (42)
Right_Hippocampus (53): linear fit = 0.62 x + 0.0 (1240 voxels, overlap=0.000)
gca peak = 0.25547 (67)
mri peak = 0.06785 (44)
Left_Hippocampus (17): linear fit = 0.65 x + 0.0 (1368 voxels, overlap=0.000)
gca peak = 0.07119 (66)
mri peak = 0.01750 (50)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (55798 voxels, overlap=0.000)
gca peak = 0.08609 (68)
mri peak = 0.01916 (39)
Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (60132 voxels, overlap=0.000)
gca peak = 0.14262 (31)
mri peak = 0.18674 (13)
Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (8201 voxels, overlap=0.000)
gca peak = 0.13649 (24)
mri peak = 0.16468 (13)
Right_Lateral_Ventricle (43): linear fit = 0.45 x + 0.0 (6387 voxels, overlap=0.000)
gca peak = 0.22151 (76)
mri peak = 0.07233 (49)
Right_Caudate (50): linear fit = 0.65 x + 0.0 (1161 voxels, overlap=0.000)
gca peak = 0.17406 (80)
mri peak = 0.09631 (51)
Left_Caudate (11): linear fit = 0.57 x + 0.0 (1311 voxels, overlap=0.000)
gca peak = 0.08500 (52)
mri peak = 0.03986 (49)
Left_Cerebellum_Cortex (8): linear fit = 0.93 x + 0.0 (37569 voxels, overlap=0.751)
gca peak = 0.10356 (55)
mri peak = 0.04679 (49)
Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (36671 voxels, overlap=0.584)
gca peak = 0.14788 (83)
mri peak = 0.05365 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.15 x + 0.0 (7690 voxels, overlap=0.068)
gca peak = 0.14909 (82)
mri peak = 0.05234 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5615 voxels, overlap=0.365)
gca peak = 0.24129 (65)
mri peak = 0.08472 (42)
Left_Amygdala (18): linear fit = 0.73 x + 0.0 (646 voxels, overlap=0.000)
gca peak = 0.29009 (65)
mri peak = 0.10817 (47)
Right_Amygdala (54): linear fit = 0.68 x + 0.0 (515 voxels, overlap=0.000)
gca peak = 0.08940 (99)
mri peak = 0.05479 (64)
Left_Thalamus_Proper (10): linear fit = 0.73 x + 0.0 (4230 voxels, overlap=0.000)
gca peak = 0.08465 (94)
mri peak = 0.06286 (65)
Right_Thalamus_Proper (49): linear fit = 0.73 x + 0.0 (3859 voxels, overlap=0.003)
gca peak = 0.09001 (85)
mri peak = 0.05409 (56)
Left_Putamen (12): linear fit = 0.57 x + 0.0 (2757 voxels, overlap=0.000)
gca peak = 0.07966 (91)
mri peak = 0.05920 (57)
Right_Putamen (51): linear fit = 0.70 x + 0.0 (2372 voxels, overlap=0.000)
gca peak = 0.18303 (100)
mri peak = 0.09630 (83)
Left_Pallidum (13): linear fit = 0.82 x + 0.0 (547 voxels, overlap=0.000)
gca peak = 0.23731 (102)
mri peak = 0.08467 (86)
Right_Pallidum (52): linear fit = 0.80 x + 0.0 (297 voxels, overlap=0.000)
gca peak = 0.06587 (83)
mri peak = 0.05241 (78)
Brain_Stem (16): linear fit = 0.88 x + 0.0 (14857 voxels, overlap=0.429)
gca peak = 0.09613 (95)
mri peak = 0.05367 (72)
Right_VentralDC (60): linear fit = 0.95 x + 0.0 (1481 voxels, overlap=0.495)
gca peak = 0.12267 (93)
mri peak = 0.04817 (88)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1663 voxels, overlap=0.302)
gca peak = 0.23067 (35)
mri peak = 0.19091 (18)
Third_Ventricle (14): linear fit = 0.50 x + 0.0 (515 voxels, overlap=0.000)
gca peak = 0.17mghWrite(aseg.auto.mgz, -1): could not open file
mri_ca_label: MRIwrite(aseg.auto.mgz) failed
757 (23)
mri peak = 0.36108 (13)
Fourth_Ventricle (15): linear fit = 0.55 x + 0.0 (640 voxels, overlap=0.000)
estimating mean gm scale to be 0.74 x + 0.0
estimating mean wm scale to be 0.80 x + 0.0
estimating mean csf scale to be 0.43 x + 0.0
27950 gm and wm labels changed (%15 to gray, %85 to white out of all changed labels)
286 hippocampal voxels changed.
1 amygdala voxels changed.
pass 1: 109498 changed. image ll: -2.337, PF=1.000
pass 2: 22418 changed. image ll: -2.336, PF=1.000
pass 3: 9759 changed.
pass 4: 5052 changed.
pass 5: 2973 changed.
26445 border labels changed to MLE ...
writing labeled volume to aseg.auto.mgz...
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
recon-all exited with ERRORS at Sat Feb 25 12:00:49 CET 2006
Fri Feb 24 16:46:33 CET 2006
/usr/local/freesurfer/subjects/fs518
/usr/local/freesurfer/bin//recon-all
-autorecon1 -s fs518
subjid fs518
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 1000000 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16375
########################################
program versions used
$Id: recon-all,v 1.8 2006/02/06 20:44:38 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:33-GMT CVS: $Id: mri_convert.c,v 1.119 2006/01/25 21:46:41 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
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: 06/02/24-15:46:33-GMT CVS: $Id: mri_normalize.c,v 1.44 2006/01/22 03:44:04 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_watershed.cpp,v 1.47 2006/01/15 22:39:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_segment.c,v 1.28 2006/02/06 20:37:32 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_fill.c,v 1.100 2006/01/18 20:01:50 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_tessellate.c,v 1.27 2006/01/30 13:27:37 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_inflate.c,v 1.30 2005/12/15 19:18:19 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_make_surfaces.c,v 1.68 2006/01/23 18:04:53 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_ca_register.c,v 1.45 2006/02/09 16:09:34 xhan Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-15:46:34-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB40_talairach_2005_12_30.gca
GCASkull RB40_talairach_with_skull_2005_12_30.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
#--------------------------------------------
#@# MotionCor Fri Feb 24 16:46:34 CET 2006
Found 2 runs
/usr/local/freesurfer/subjects/fs518/mri/orig/001.mgz
/usr/local/freesurfer/subjects/fs518/mri/orig/002.mgz
/usr/local/freesurfer/subjects/fs518
mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/fs518/mri/orig/001.mgz /usr/local/freesurfer/subjects/fs518/mri/orig/002.mgz
tmpdir is /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511
--------------------------------------------------------------
mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz.mri_motion_correct.fsl.log
--------------------------------------------------------------
-----------------------------------------
Converting /usr/local/freesurfer/subjects/fs518/mri/orig/001.mgz
Fri Feb 24 16:46:43 CET 2006
/usr/local/freesurfer/subjects/fs518
mri_convert /usr/local/freesurfer/subjects/fs518/mri/orig/001.mgz /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.img -odt float
reading from /usr/local/freesurfer/subjects/fs518/mri/orig/001.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.img...
Analyze Output Matrix
0.000 0.000 1.400 -88.834;
-0.938 0.000 0.000 153.913;
0.000 -0.938 0.000 124.743;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /usr/local/freesurfer/subjects/fs518/mri/orig/002.mgz
Fri Feb 24 16:46:45 CET 2006
/usr/local/freesurfer/subjects/fs518
mri_convert /usr/local/freesurfer/subjects/fs518/mri/orig/002.mgz /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img -odt float
reading from /usr/local/freesurfer/subjects/fs518/mri/orig/002.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img...
Analyze Output Matrix
0.000 0.000 1.400 -88.834;
-0.938 0.000 0.000 153.913;
0.000 -0.938 0.000 124.743;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img
Fri Feb 24 16:46:46 CET 2006
/usr/local/freesurfer/subjects/fs518
fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.img -i /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img -o /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.img -tmpdir /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511 -cleanup
\n\n
$Id: fsl_rigid_register,v 1.13 2006/01/24 19:51:34 greve Exp $
Fri Feb 24 16:46:47 CET 2006
/usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.img
Reference is analyze, not converting
Input is analyze, not converting
Output is analyze, not converting
--------------------------------------
/usr/local/freesurfer/subjects/fs518
calling eval flirt -in /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.hdr -out /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.hdr -omat /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.fslmat
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
Started at Fri Feb 24 16:46:47 CET 2006
Ended at Fri Feb 24 16:55:03 CET 2006
fsl_rigid_register Done
To check results, run:
tkmedit -f /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.img -aux /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.img
mv /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/resampled.img /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img
-----------------------------------------
Averaging
Fri Feb 24 16:55:03 CET 2006
/usr/local/freesurfer/subjects/fs518
inhibiting isotropic volume interpolation
1 of 2: reading /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-1.img...
2 of 2: reading /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/cor-2.img...
writing to /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/avgvol.img...
alignment and averaging took 0 minutes and 18 seconds.
INFO: analyzeRead(): min = 0, max = 2726
INFO: analyzeRead(): min = 0, max = 1924.71
Analyze Output Matrix
0.000 0.000 1.400 -88.834;
-0.938 0.000 0.000 153.913;
0.000 -0.938 0.000 124.743;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting Average to output
Fri Feb 24 16:55:21 CET 2006
/usr/local/freesurfer/subjects/fs518
mri_convert /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/avgvol.img /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz -tr 9.452 -te 2.212 -TI 450 -flip_angle 0.122173
mri_convert /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/avgvol.img /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz -tr 9.452 -te 2.212 -TI 450 -flip_angle 0.122173
reading from /usr/local/freesurfer/subjects/fs518/mri/tmp-mri_motion_correct.fsl-29511/avgvol.img...
INFO: analyzeRead(): min = 0, max = 1828.89
TR=9.45, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz...
-----------------------------------------
Started at: Fri Feb 24 16:46:36 CET 2006
Ended at: Fri Feb 24 16:55:38 CET 2006
mri_motion_correct.fsl: done
/usr/local/freesurfer/subjects/fs518
mri_convert /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz /usr/local/freesurfer/subjects/fs518/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz /usr/local/freesurfer/subjects/fs518/mri/orig.mgz --conform
reading from /usr/local/freesurfer/subjects/fs518/mri/rawavg.mgz...
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, 0, 0)
Original Data has (0.9375, 0.9375, 1.4) mm size and (256, 256, 124) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 3 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/fs518/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/fs518/mri/orig.mgz /usr/local/freesurfer/subjects/fs518/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Fri Feb 24 16:56:12 CET 2006
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/fs518/mri
/usr/local/freesurfer/bin//mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
Fri Feb 24 16:56:12 CET 2006
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
tmpdir is ./tmp.mri_nu_correct.mni.30413
/usr/local/freesurfer/subjects/fs518/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30413/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30413/nu0.mnc
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from orig.mgz...
Talairach transform /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm ...which does not exist
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to ./tmp.mri_nu_correct.mni.30413/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Feb 24 16:56:27 CET 2006
nu_correct -clobber ./tmp.mri_nu_correct.mni.30413/nu0.mnc ./tmp.mri_nu_correct.mni.30413/nu1.mnc
[martin@localhost:/usr/local/freesurfer/subjects/fs518/mri/] [2006-02-24 16:56:27] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /home/martin/tmp/nu_correct_30473/ ./tmp.mri_nu_correct.mni.30413/nu0.mnc ./tmp.mri_nu_correct.mni.30413/nu1.imp
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 2
CV of field change: 0.000397117
[martin@localhost:/usr/local/freesurfer/subjects/fs518/mri/] [2006-02-24 16:56:36] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30413/nu0.mnc /home/martin/tmp/nu_correct_30473//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
--------------------------------------------------------
Iteration 2 Fri Feb 24 16:56:46 CET 2006
nu_correct -clobber ./tmp.mri_nu_correct.mni.30413/nu1.mnc ./tmp.mri_nu_correct.mni.30413/nu2.mnc
[martin@localhost:/usr/local/freesurfer/subjects/fs518/mri/] [2006-02-24 16:56:47] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /home/martin/tmp/nu_correct_30584/ ./tmp.mri_nu_correct.mni.30413/nu1.mnc ./tmp.mri_nu_correct.mni.30413/nu2.imp
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 2
CV of field change: 0.00034035
[martin@localhost:/usr/local/freesurfer/subjects/fs518/mri/] [2006-02-24 16:56:55] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30413/nu1.mnc /home/martin/tmp/nu_correct_30584//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
mri_convert ./tmp.mri_nu_correct.mni.30413/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.30413/nu2.mnc nu.mgz --like orig.mgz
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from ./tmp.mri_nu_correct.mni.30413/nu2.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
Talairach transform /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm ...which does not exist
writing to nu.mgz...
Fri Feb 24 16:57:33 CET 2006
mri_nu_correct.mni done
#--------------------------------------------
#@# Talairach Fri Feb 24 16:57:33 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/usr/local/freesurfer/subjects/fs518/mri
/usr/local/freesurfer/bin//talairach
--i nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
Fri Feb 24 16:57:34 CET 2006
tmpdir is transforms/tmp.talairach.30759
/usr/local/freesurfer/subjects/fs518/mri
mri_convert nu.mgz transforms/tmp.talairach.30759/src.mnc
mri_convert nu.mgz transforms/tmp.talairach.30759/src.mnc
Can't find the talairach xform '/usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm'
Transform is not loaded into mri
reading from nu.mgz...
Talairach transform /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm does not exist ...
... trying /usr/local/freesurfer/subjects/fs518/mri/transforms/talairach.xfm ...which does not exist
TR=9.45, TE=2.21, TI=450.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.30759/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30759/src.mnc transforms/talairach.auto.xfm
Fri Feb 24 16:58:46 CET 2006
talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Intensity Normalization Fri Feb 24 16:58:47 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
0.831 0.638 0.186 -25.408;
-0.588 0.874 -0.370 -33.483;
-0.317 0.157 0.875 -28.797;
0.000 0.000 0.000 1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to T1.mgz
3D bias adjustment took 11 minutes and 32 seconds.
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
#--------------------------------------------
#@# Skull Stripping Fri Feb 24 17:10:24 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
mri_watershed -atlas T1.mgz brainmask.auto.mgz
Mode: Atlas analysis
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C
*************************WATERSHED**************************
preflooding height equal to 25 percent
Sorting...
T1-weighted MRI image
modification of the preflooding height to 15 percent
Count how many 110 voxels are present : 104362
Find the largest 110-component...
heap usage = 165908 Kbytes.
removing small segments (less than 1 percent of maxarea).done
And identify it as the main brain basin...done
Main component: 89334 voxels
first estimation of the COG coord: x=132 y=96 z=120 r=100
first estimation of the main basin volume: 4256226 voxels
global maximum in x=165, y=95, z=80, Imax=255
CSF=23, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
done
Analyze
main basin size= 1450676 voxels, voxel volume =1.000
= 1450676 mmm3 = 1450.676 cm3
done
PostAnalyze...
ambiguous basin, merged: at least 17 ambiguous voxels; size: 4558 voxels
***** 1 basin(s) merged in 2 iteration(s)
***** 4558 voxel(s) added to the main basin
done
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=131,y=99, z=116, r=10266 iterations
Problem with the least square interpolation in GM_MIN calculation.
before analyzing : CSF_MAX=47, TRANSITION=36, GM_MIN=26, GM=53
after analyzing : CSF_MAX=31, TRANSITION=36, GM_MIN=36, GM=40
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...68 iterations
*********************VALIDATION*********************
Rigid alignment...
scanning 32.00 degree nbhd, min sse = 3.73 at ( 8.00, -8.00, 0.00)
scanning 16.00 degree nbhd, min sse = 3.73 at ( 0.00, 0.00, 0.00)
scanning 8.00 degree nbhd, min sse = 3.63 at (-2.00, 2.00, -2.00)
scanning 4.00 degree nbhd, min sse = 3.62 at ( 1.00, 0.00, 0.00)
done
before rotation: sse = 4.68, sigma = 8.76
after rotation: sse = 3.62, sigma = 7.60
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 4.70, its var is 15.85
before Erosion-Dilatation 4.20% of inacurate vertices
after Erosion-Dilatation 7.38% of inacurate vertices
23.81% of 'positive' inacurate vertices
76.19% of 'negative' inacurate vertices
THE SEGMENTATION IS PROBABLY NOT CORRECT
Scaling of atlas fields onto current surface fields
Correcting the shape of the surface...38 iterations
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...
mri_strip_skull: done peeling brainComputing COG for corrected surface
Initial Configuration: NRG=18229.074156, ( -3.725646 , 20.892566 , 32.861635 )
Final Minimum found: NRG=16697.966426, ( -3.448698 , 21.252604 , 31.778001 )done
The shape of the surface was incorrect,
hence we rigidly realign the surface with the template
Rigid alignment...
scanning 32.00 degree nbhd, min sse = 0.73 at ( 8.00, -8.00, 0.00)
scanning 16.00 degree nbhd, min sse = 0.64 at ( 0.00, 4.00, -4.00)
scanning 8.00 degree nbhd, min sse = 0.45 at (-2.00, -2.00, 2.00)
scanning 4.00 degree nbhd, min sse = 0.45 at ( 0.00, 0.00, -1.00)
done
before rotation: sse = 2.38, sigma = 4.80
after rotation: sse = 0.45, sigma = 0.85
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 0.45, its var is 0.62
before Erosion-Dilatation 0.00% of inacurate vertices
after Erosion-Dilatation 0.00% of inacurate vertices
Validation of the shape of the surface done.67 iterations
mri_strip_skull: done peeling brain
Brain Size = 1480308 voxels, voxel volume = 1.000 mm3
= 1480308 mmm3 = 1480.308 cm3
******************************
Save...done
INFO: Fixing vertex area
cp brainmask.auto.mgz brainmask.mgz
#------------------------------------------
recon-all finished without error at Fri Feb 24 17:27:01 CET 2006
New invocation of recon-all
Fri Feb 24 17:58:53 CET 2006
/usr/local/freesurfer/subjects/fs518
/usr/local/freesurfer/bin//recon-all
-autorecon2 -s fs518
subjid fs518
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 1000000 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16375
########################################
program versions used
$Id: recon-all,v 1.8 2006/02/06 20:44:38 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_convert.c,v 1.119 2006/01/25 21:46:41 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
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: 06/02/24-16:58:53-GMT CVS: $Id: mri_normalize.c,v 1.44 2006/01/22 03:44:04 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_watershed.cpp,v 1.47 2006/01/15 22:39:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_segment.c,v 1.28 2006/02/06 20:37:32 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_fill.c,v 1.100 2006/01/18 20:01:50 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_tessellate.c,v 1.27 2006/01/30 13:27:37 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_inflate.c,v 1.30 2005/12/15 19:18:19 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_make_surfaces.c,v 1.68 2006/01/23 18:04:53 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_ca_register.c,v 1.45 2006/02/09 16:09:34 xhan Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/02/24-16:58:53-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: UNKNOWN Machine: localhost Platform: Linux PlatformVersion: 2.6.12-15mdk CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB40_talairach_2005_12_30.gca
GCASkull RB40_talairach_with_skull_2005_12_30.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
#-------------------------------------
#@# EM Registration Fri Feb 24 17:58:54 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
average std = 7.0 using min determinant for regularization = 4.9
0 singular and 1794 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
total sample mean = 85.3 (517 zeros)
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2400, passno 0, spacing 8
************************************************
First Search limited to translation only.
************************************************
Found translation: (-8.5, 21.0, -16.5): log p = -49510.3
Result so far: scale 1.000: max_log_p=-30743.7, old_max_log_p =-49510.3 (thresh=-49460.8)
1.184 0.165 0.023 -52.092;
-0.157 1.103 0.155 13.187;
0.000 -0.147 1.044 -7.552;
0.000 0.000 0.000 1.000;
Result so far: scale 1.000: max_log_p=-29313.3, old_max_log_p =-30743.7 (thresh=-30712.9)
1.096 0.192 -0.111 -26.730;
-0.165 1.139 0.318 -8.935;
0.186 -0.273 1.006 -8.124;
0.000 0.000 0.000 1.000;
Result so far: scale 1.000: max_log_p=-29313.3, old_max_log_p =-29313.3 (thresh=-29284.0)
1.096 0.192 -0.111 -26.730;
-0.165 1.139 0.318 -8.935;
0.186 -0.273 1.006 -8.124;
0.000 0.000 0.000 1.000;
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.09606 0.19194 -0.11064 -26.72957;
-0.16474 1.13905 0.31757 -8.93471;
0.18631 -0.27306 1.00605 -8.12422;
0.00000 0.00000 0.00000 1.00000;
nsamples 2400
Quasinewton: input matrix
1.09606 0.19194 -0.11064 -26.72957;
-0.16474 1.13905 0.31757 -8.93471;
0.18631 -0.27306 1.00605 -8.12422;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
fp = 29264.986328, fret = 29264.986328, ftol = 0.000010, EPS = 0.000000
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.09606 0.19194 -0.11064 -26.72957;
-0.16474 1.13905 0.31757 -8.93471;
0.18631 -0.27306 1.00605 -8.12422;
0.00000 0.00000 0.00000 1.00000;
nsamples 250643
Quasinewton: input matrix
1.09606 0.19194 -0.11064 -26.72957;
-0.16474 1.13905 0.31757 -8.93471;
0.18631 -0.27306 1.00605 -8.12422;
0.00000 0.00000 0.00000 1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
freeing gibbs priors...done.
bounding unknown intensity as < 14.7 or > 943.6
************************************************
spacing=8, using 2400 sample points, tol=1.00e-05...
************************************************
Note: program considers input volume #1 as the most T1-like
using real data threshold=29.0
using (110, 80, 123) as brain centroid...
mean wm in atlas = 106, using box (94,65,103) --> (126, 95,143) to find MRI wm
before smoothing, mri peak at 78
after smoothing, mri peak at 78, scaling input intensities by 1.364
scaling channel 0 by 1.36415
initial log_p = -109234.6
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
****************************************
Nine parameter search. iteration 2 nscales = 2 ...
****************************************
reducing scale to 0.2500
***********************************************
Computing MAP estimate using 2400 samples...
***********************************************
dfp_em_step_func: 003: -log(p) = 29313.3
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 004: -log(p) = 29284.5
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 005: -log(p) = 29266.4
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 006: -log(p) = 29265.0
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
outof QuasiNewtonEMA: 008: -log(p) = 29265.0 tol 0.000010
Resulting transform:
1.096 0.192 -0.111 -26.730;
-0.165 1.139 0.318 -8.935;
0.186 -0.273 1.006 -8.124;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -29313.3 (old=-109234.6)
transform before final EM align:
1.096 0.192 -0.111 -26.730;
-0.165 1.139 0.318 -8.935;
0.186 -0.273 1.006 -8.124;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 250643 samples.
**************************************************
dfp_em_step_func: 007: -log(p) = 3035022.0
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 008: -log(p) = 2994399.0
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 009: -log(p) = 2965236.2
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 010: -log(p) = 2947334.5
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.01, -8.12)
dfp_em_step_func: 011: -log(p) = 2940430.5
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.00, -8.12)
dfp_em_step_func: 012: -log(p) = 2927773.0
after pass:transform: ( 1.10, 0.19, -0.11, -26.73)
( -0.16, 1.14, 0.32, -8.93)
( 0.19, -0.27, 1.00, -8.12)
outof QuasiNewtonEMA: 014: -log(p) = 2927285.0 tol 0.000000
final transform:
1.100 0.195 -0.104 -26.730;
-0.159 1.142 0.321 -8.935;
0.185 -0.274 1.004 -8.124;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta...
registration took 19 minutes and 38 seconds.
#--------------------------------------
#@# CA Normalize Fri Feb 24 18:18:35 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.lta norm.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
reading transform from 'transforms/talairach.lta'...
INFO: compute sample coordinates transform
1.100 0.195 -0.104 -26.730;
-0.159 1.142 0.321 -8.935;
0.185 -0.274 1.004 -8.124;
0.000 0.000 0.000 1.000;
INFO: transform used
reading input volume from nu.mgz...
Note: program considers input volume #1 as the most T1-like
using real data threshold=29.0
using (110, 80, 123) as brain centroid...
mean wm in atlas = 106, using box (94,65,103) --> (126, 95,143) to find MRI wm
before smoothing, mri peak at 78
after smoothing, mri peak at 78, scaling input intensities by 1.364
scaling channel 0 by 1.36415
using 250643 sample points...
finding control points in Left_Cerebral_White_Matter....
found 42041 control points for structure...
bounding box (124, 45, 39) --> (189, 144, 197)
Left_Cerebral_White_Matter: limiting intensities to 137.0 --> 153.0
116 of 157 (73.9%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 41886 control points for structure...
bounding box (71, 42, 43) --> (139, 134, 201)
Right_Cerebral_White_Matter: limiting intensities to 135.0 --> 157.0
151 of 168 (89.9%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 2779 control points for structure...
bounding box (122, 119, 69) --> (158, 158, 123)
Left_Cerebellum_White_Matter: limiting intensities to 116.0 --> 124.0
38 of 44 (86.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2673 control points for structure...
bounding box (84, 120, 72) --> (125, 151, 127)
Right_Cerebellum_White_Matter: limiting intensities to 127.0 --> 135.0
45 of 54 (83.3%) samples deleted
finding control points in Brain_Stem....
found 3627 control points for structure...
bounding box (111, 106, 105) --> (144, 164, 138)
Brain_Stem: limiting intensities to 116.0 --> 124.0
91 of 97 (93.8%) samples deleted
using 520 total control points for intensity normalization...
bias field = 0.749 +- 0.050
0 of 79 control points discarded
writing normalized volume to norm.mgz...
freeing GCA...done.
normalization took 3 minutes and 5 seconds.
#--------------------------------------
#@# CA Reg Fri Feb 24 18:21:41 CET 2006
/usr/local/freesurfer/subjects/fs518/mri
mri_ca_register -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca transforms/talairach.m3z
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB40_talairach_2005_12_30.gca'...
setting gca type = Normal gca type
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
renormalizing by structure alignment....
renormalizing input #0
aligning Right_Cerebral_White_Matter...
source mean =68.9044, std = 17.0047
X:68-143; Y:40-138; Z:40-205
gca peak = 0.05458 (115)
mri peak = 0.04757 (84)
Right_Cerebral_White_Matter (41): linear fit = 0.77 x + 0.0 (95940 voxels, overlap=0.071)
aligning Left_Cerebral_White_Matter...
source mean =68.4889, std = 16.763
X:121-194; Y:42-148; Z:36-202
gca peak = 0.05666 (115)
mri peak = 0.02982 (84)
uniform distribution in MR - rejecting arbitrary fit
aligning Right_Hippocampus...
source mean =67.9981, std = 15.1827
X:93-126; Y:100-125; Z:99-151
gca peak = 0.11828 (64)
mri peak = 0.07114 (40)
overlap = 0.000123142, overlap_threshold = 0.001
insufficient overlap 0.0001 in histograms - rejecting
aligning Left_Hippocampus...
source mean =75.7372, std = 21.541
X:134-167; Y:107-133; Z:94-147
gca peak = 0.16548 (65)
mri peak = 0.06831 (45)
Left_Hippocampus (17): linear fit = 0.68 x + 0.0 (2522 voxels, overlap=0.002)
aligning Left_Cerebral_Cortex...
gca peak = 0.05861 (67)
mri peak = 0.02245 (40)
uniform distribution in MR - rejecting arbitrary fit
aligning Right_Cerebral_Cortex...
gca peak = 0.06315 (69)
mri peak = 0.01771 (38)
uniform distribution in MR - rejecting arbitrary fit
aligning Left_Lateral_Ventricle...
source mean =72.1977, std = 35.9622
X:131-162; Y:81-126; Z:66-162
gca peak = 0.05355 (17)
mri peak = 0.11181 (11)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (10085 voxels, overlap=0.069)
aligning Right_Lateral_Ventricle...
source mean =61.4245, std = 27.6567
X:95-140; Y:77-119; Z:67-167
gca peak = 0.06083 (18)
mri peak = 0.13755 (12)
Right_Lateral_Ventricle (43): linear fit = 0.55 x + 0.0 (7741 voxels, overlap=0.143)
aligning Right_Caudate...
source mean =69.2955, std = 28.1481
X:114-136; Y:76-104; Z:110-166
gca peak = 0.10620 (72)
mri peak = 0.07148 (46)
Right_Caudate (50): linear fit = 0.65 x + 0.0 (2703 voxels, overlap=0.198)
aligning Left_Caudate...
source mean =78.3629, std = 38.8572
X:136-158; Y:81-108; Z:104-162
gca peak = 0.11131 (84)
mri peak = 0.06377 (52)
overlap = 0.000132012, overlap_threshold = 0.001
insufficient overlap 0.0001 in histograms - rejecting
aligning Left_Cerebellum_Cortex...
source mean =52.1614, std = 19.6356
X:116-174; Y:110-175; Z:55-123
gca peak = 0.06541 (56)
mri peak = 0.04081 (46)
Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (36279 voxels, overlap=0.200)
aligning Right_Cerebellum_Cortex...
source mean =51.48, std = 19.5333
X:71-132; Y:109-170; Z:58-128
gca peak = 0.07158 (57)
mri peak = 0.04300 (52)
Right_Cerebellum_Cortex (47): linear fit = 0.88 x + 0.0 (31385 voxels, overlap=0.451)
aligning Left_Cerebellum_White_Matter...
source mean =65.0878, std = 18.5658
X:119-162; Y:117-162; Z:66-127
gca peak = 0.07712 (87)
mri peak = 0.05738 (76)
Left_Cerebellum_White_Matter (7): linear fit = 0.90 x + 0.0 (8368 voxels, overlap=0.556)
aligning Right_Cerebellum_White_Matter...
source mean =67.1531, std = 16.9414
X:81-129; Y:117-155; Z:70-131
gca peak = 0.09487 (84)
mri peak = 0.07908 (80)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5364 voxels, overlap=0.768)
aligning Left_Amygdala...
source mean =66.3207, std = 19.6912
X:135-163; Y:110-132; Z:128-152
gca peak = 0.11798 (62)
mri peak = 0.04641 (37)
Left_Amygdala (18): linear fit = 0.60 x + 0.0 (478 voxels, overlap=0.001)
aligning Right_Amygdala...
source mean =63.5113, std = 13.2111
X:100-127; Y:104-126; Z:133-156
gca peak = 0.15512 (63)
mri peak = 0.04272 (45)
overlap = 0.00079709, overlap_threshold = 0.001
insufficient overlap 0.0008 in histograms - rejecting
aligning Left_Thalamus_Proper...
source mean =81.4102, std = 30.8407
X:130-157; Y:89-121; Z:99-141
gca peak = 0.06295 (104)
mri peak = 0.03771 (58)
Left_Thalamus_Proper (10): linear fit = 0.62 x + 0.0 (6262 voxels, overlap=0.040)
aligning Right_Thalamus_Proper...
source mean =75.5643, std = 26.984
X:106-137; Y:85-114; Z:104-142
gca peak = 0.06253 (102)
mri peak = 0.03806 (61)
Right_Thalamus_Proper (49): linear fit = 0.80 x + 0.0 (7004 voxels, overlap=0.189)
aligning Left_Putamen...
source mean =92.231, std = 15.3145
X:138-169; Y:91-123; Z:112-159
gca peak = 0.06876 (82)
mri peak = 0.04777 (63)
Left_Putamen (12): linear fit = 0.68 x + 0.0 (3435 voxels, overlap=0.025)
aligning Right_Putamen...
source mean =82.0424, std = 10.3166
X:99-129; Y:82-113; Z:119-165
gca peak = 0.06949 (87)
mri peak = 0.03793 (57)
Right_Putamen (51): linear fit = 0.68 x + 0.0 (3804 voxels, overlap=0.118)
aligning Left_Pallidum...
source mean =89.9532, std = 23.1939
X:140-161; Y:96-118; Z:119-149
gca peak = 0.11762 (98)
mri peak = 0.09040 (94)
Left_Pallidum (13): linear fit = 0.90 x + 0.0 (215 voxels, overlap=0.142)
aligning Right_Pallidum...
source mean =81.175, std = 16.8616
X:106-130; Y:89-110; Z:125-152
gca peak = 0.16855 (106)
mri peak = 0.12772 (85)
Right_Pallidum (52): linear fit = 0.80 x + 0.0 (361 voxels, overlap=0.002)
aligning Brain_Stem...
source mean =65.9659, std = 25.9574
X:108-148; Y:104-168; Z:102-142
gca peak = 0.04887 (88)
mri peak = 0.05461 (72)
Brain_Stem (16): linear fit = 0.82 x + 0.0 (15780 voxels, overlap=0.289)
aligning Right_VentralDC...
source mean =73.9926, std = 22.2512
X:103-137; Y:98-122; Z:111-149
gca peak = 0.05769 (94)
mri peak = 0.05089 (85)
Right_VentralDC (60): linear fit = 0.88 x + 0.0 (2037 voxels, overlap=0.298)
aligning Left_VentralDC...
source mean =78.5816, std = 25.868
X:127-158; Y:99-126; Z:107-148
gca peak = 0.05759 (95)
mri peak = 0.03981 (82)
Left_VentralDC (28): linear fit = 0.85 x + 0.0 (2882 voxels, overlap=0.200)
aligning Third_Ventricle...
source mean =57.7557, std = 21.8007
X:126-141; Y:93-116; Z:108-149
gca peak = 0.14462 (29)
mri peak = 0.07945 (26)
Third_Ventricle (14): linear fit = 0.90 x + 0.0 (461 voxels, overlap=0.560)
aligning Fourth_Ventricle...
source mean =50.9124, std = 17.7859
X:112-135; Y:109-159; Z:95-119
gca peak = 0.11044 (27)
mri peak = 0.08769 (17)
Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (1048 voxels, overlap=0.343)
estimating mean gm scale to be 0.68 x + 0.0
estimating mean wm scale to be 0.77 x + 0.0
estimating mean csf scale to be 0.64 x + 0.0
writing gca to talairach.gca...
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
pct change decreased
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
rms increased - undoing step...
pct change < tol 0.025, nsmall = 2 of 2
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change decreased
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
rms increased - undoing step...
setting smoothness coefficient to 0.40
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 1.00
blurring input image with Gaussian with sigma=2.000...
pct change decreased
switching integration type to fixed (done=0)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
resetting metric properties...
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
pct change decreased
switching integration type to fixed (done=0)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
rms increased - undoing step...
blurring input image with Gaussian with sigma=0.500...
pct change decreased
switching integration type to fixed (done=1)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
rms increased - undoing step...
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
pct change decreased
pct change < tol 0.025, nsmall = 1 of 2
pct change < tol 0.025, nsmall = 2 of 2
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
pct change < tol 0.025, nsmall = 1 of 2
rms increased - undoing step...
pct change < tol 0.025, nsmall = 2 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
switching integration type to fixed (done=1)
rms increased - undoing step...
pct change < tol 0.025, nsmall = 1 of 2
blurring input image with Gaussian with sigma=0.500...
switching integration type to fixed (done=1)Segmentation fault (core dumped)
ERROR: mri_ca_register with non-zero status
Linux localhost 2.6.12-15mdk #1 Mon Jan 9 23:59:19 MST 2006 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ unknown GNU/Linux
recon-all exited with ERRORS at Sat Feb 25 10:29:42 CET 2006
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