Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Freesurfer tutorial
by Gabe Castillo 27 Feb '06

27 Feb '06

Hello, I am new to using freesurfer. I have installed it successfully and am attempting to go through the tutorial. The tutorial seems to be out of date. I am at the "Data Conversion" step of the tutorial with the tutorial_subjs directory from the gzipped buckner_data tarball. If I try to run "recon-all -i 014-anon/001.dcm -i 015-anon/001.dcm -s anon" it complains about the "-i" flag. It also complained about the "-autorecon-all" and "-autrecon1" flags. Looking through the usage output, I'm guessing that these have been replaced by "-all" and "-stage1" respectively. What has the "-i" flag been changed too. Forgive my ignorance, if anybody has a changelog or can point me to one, I'd be happy to dig around for this info. Thanks, Gabe Castillo

2 1

tkregister2 woes
by Sebastian Moeller 27 Feb '06

27 Feb '06

Aloha fellow Surfers, while testing the dev20060224 centos4_x86_64 release I stumbled upon some issues with tkregister2. That is tkregister2 produces X errors leading to a black screen once the image window is clicked into. Since I try to cheat monkey data into the freesurfer chain I use tkregister2 to register my structurals with some atlas based assumptions (basically rotating the volume slightly around three axis). Then I use mri_vol2vol to reslice a new rotated volume. And this is where tkregister2 chokes: Received X error ! Error code : 10 Request code : 89 Minor code : 0 Error test : ´BadAccess (attempt to access private resource denied)´ There are plenty of these errors, and once the image window is clicked into the screen turns black, only the mouse survives. Remotly login in and killing the tkregister2 process gives back control over the machine. Any hints besides "don't do that then" ;)? ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

3 2

problems with SubCort seg and CA Reg
by Martin Ystad 27 Feb '06

27 Feb '06

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

2 1

freesurfer and debian "etch"
by wilms 26 Feb '06

26 Feb '06

Dear all, does someone out there run freesurfer (freesurfer-Linux-rh9-dev20060210-full.tar.gz) under debian etch? Installation runs smoothly, however, when I test the freesurfer installation with medpc32:~$ tksurfer bert rh pial only a tiny fraction of Bert's brain is displayed. The GUI otherwise seems to work as I can rotate etc this brain fraction. I installed the same freesurfer version on a different computer running debian "sarge", which is the current stable distribution. - Here, I can see the whole brain! As suggested elsewhere I thus compared the shared library dependencies using medpc32:~$ ldd `which tkmedit` Here is what I got: ######### "etch"-machine: ######### medpc32:~$ ldd `which tkmedit` linux-gate.so.1 => (0xffffe000) libtix8.1.8.3.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtix8.1.8.3.so (0xb7fb0000) libtk8.4.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtk8.4.so (0xb7ef0000) libtcl8.4.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtcl8.4.so (0xb7e57000) libglut.so.3 => /usr/lib/libglut.so.3 (0xb7e0d000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0xb7e04000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0xb7dec000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0xb7dd6000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0xb7dce000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d4f000) libGL.so.1 => /usr/lib/libGL.so.1 (0xb7ceb000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0xb7c20000) libgsl.so.0 => /local/opt/freesurfer_dev20060210/lib/gsl/lib/libgsl.so.0 (0xb7acc000) libgslcblas.so.0 => /local/opt/freesurfer_dev20060210/lib/gsl/lib/libgslcblas.so.0 (0xb7a9c000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb7a7c000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb7a2a000) libz.so.1 => /usr/lib/libz.so.1 (0xb7a15000) libm.so.6 => /lib/tls/libm.so.6 (0xb79ef000) libcrypt.so.1 => /lib/tls/libcrypt.so.1 (0xb79c1000) libc.so.6 => /lib/tls/libc.so.6 (0xb788a000) libdl.so.2 => /lib/tls/libdl.so.2 (0xb7886000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0xb7878000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0xb7827000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb774a000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb773f000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0xb772d000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0xb7728000) /lib/ld-linux.so.2 (0xb7feb000) ######### "sarge" machine: ######### kogneuro-web:~$ ldd `which tkmedit` libtix8.1.8.3.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0xb7fae000) libtk8.4.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0xb7eee000) libtcl8.4.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0xb7e55000) libglut.so.3 => /usr/lib/libglut.so.3 (0xb7e1b000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0xb7e12000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0xb7dfb000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0xb7de4000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0xb7ddc000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d61000) libGL.so.1 => /usr/lib/libGL.so.1 (0xb7cf2000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0xb7c2b000) libgsl.so.0 => /local/data/tools/freesurfer/lib/gsl/lib/libgsl.so.0 (0xb7ad7000) libgslcblas.so.0 => /local/data/tools/freesurfer/lib/gsl/lib/libgslcblas.so.0 (0xb7aa6000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb7a88000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb7a38000) libz.so.1 => /usr/lib/libz.so.1 (0xb7a26000) libm.so.6 => /lib/tls/libm.so.6 (0xb7a04000) libcrypt.so.1 => /lib/tls/libcrypt.so.1 (0xb79d7000) libc.so.6 => /lib/tls/libc.so.6 (0xb78a1000) libdl.so.2 => /lib/tls/libdl.so.2 (0xb789e000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0xb7890000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0xb783f000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb7785000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7779000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0xb776a000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0xb7fea000) The differences seem to be: ######### "etch" machine: ######### libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb774a000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0xb7728000) /lib/ld-linux.so.2 (0xb7feb000) ######### "sarge" machine: ######### libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb7785000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0xb7fea000) Does this mean that the c++ libraries on my etch-running machine are "too" new? Why is there no "=>" for /lib/ld-linux.so.2 on my etch-running machine? I would greatly appreciate any comments or ideas what else I could do. Many thanks in advance, Marcus -- ------------------------------- Dr. Marcus Wilms Cognitive Neurology Group Institute of Medicine Forschungszentrum Juelich 52425 Juelich, Germany Phone: +49 (02461) 61-6184 E-Mail: ma.wilms(a)fz-juelich.de Home: http://www.netwilms.net ----------------------------><>

4 4

paint, mri_vol2surf, paint-sess
by Don Hagler 23 Feb '06

23 Feb '06

I tried painting to a surface created with the new recon-all (using paint or mri_vol2surf (version 1.22 2005/07/05)), and it seems that the surrfaces are not being read correctly (the data in the w file has the speckled appearance you get when the vertex numbers are wrong). I posted a message before about my fieldsign code not working on the new surfaces and Bruce Fischl said this about the different surfaces (i.e. orig, smoothwm, inflated, etc.): "check the # of vertices etc... with mris_euler_number (or mris_info). Make sure they all are the same. The file sizes aren't necessarily the same any more as they contain additional info, but the # of vertices etc. should be invariant." So are paint and mri_vol2surf still supported under the current distribution of MGH FreeSurfer? Are there newer versions out there? Or is everyone using paint-sess these days? By the way, what was done to the format of the surfaces? What additional info do they contain? Is there documentation or posted code on how to read the new surfaces?

1 1

tkregister2 talairach target
by Doug Greve 23 Feb '06

23 Feb '06

Starting tomorrow (Fri), those using nmr-dev will notice a different talairach volume when checking/editing your talairach registration with tkregister2, eg, tkregister2 --fstal --s bert Previously, it used $SUBJECTS_DIR/talairach/mri/orig.mgz Now, it uses $FREESURFER_HOME/average/mni305.cor.mgz The old one was an average that was created a long time ago. The new one is the actual MNI 305 template that is used during automatic talairach registration done in recon-all. We are changing the target because it is better to use the actual template than a surrogate. We are changing it now in anticipation of the (soon) new freesurfer release (!). You should not need to modify your talairach.xfm based on the new target, as the true template and the surrogate are quite close to each other. You can see by comparing the old and new by running: tkregister2 --fstal --s talairach (you will not be able to save any edits :). doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

mghWrite error
by Nguyen, Thang Q 23 Feb '06

23 Feb '06

Hello all, I have a few scans I need to convert using mri_convert but I receive this error: writing to 2.mgh... mghWrite(2.mgh, -1): could not open file ERROR: failure writing 2.mgh I can convert other images from the same scanner, same subject, same header without any problems but the few that I have recently tried to convert have this issue. I can view the images in tkmedit so I don't believe there is an issue with the images themselves. What does this error mean and how can I override it? Thank you all for your input, Thang Nguyen ------------------------ Thang Nguyen Biomedical Informatics Research Network Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine

2 1

label_child memory erro
by hwier＠uchicago.edu 23 Feb '06

23 Feb '06

Hi, I'm running freesurfer (version 0.9, 33y) and I'm trying to run the label_child script I found in the bin directory, however I'm getting the following error(where my subject directory is called 205): ---------------- Command Line: > label_child 205 ---------------- Output: using gca /opt/freesurfer_alpha/average/talairach_children_tl_b.gca to label thin temporal lobe... using /nfs/raidzone/data/NL-GCS/subjects/freesurfer//205/mri/brain to mask final labeling... reading 1 input volumes... reading classifier array from /opt/freesurfer_alpha/average/talairach_children_b.gca... GCAread(/opt/freesurfer_alpha/average/talairach_children_b.gca): couldn't expand gcs to 286990032 Cannot allocate memory ------------------- My computers' resources (from /proc/meminfo) are: MemTotal: 4148928 kB MemFree: 871196 kB Can my computer handle running label_child? Am I just calling something incorrectly? Is there anything I could try to change in order to get label_child to run? Thanks, Helen.

2 1

troubles with monkey brains (inflate)
by Sebastian Moeller 22 Feb '06

22 Feb '06

Dear all, at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing? Ahoi & Thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

2 3

file paths in mgz headers
by Glenn Lawyer 22 Feb '06

22 Feb '06

Hi, We like to structure our work by putting all scans into a batch account and doing recon-all -autorecon1 -autorecon2. We then transfer the scans to our individual accounts to check the quality before running the rest of the processing stream. This creates a small problem, in that the full path to the talairach.xfm is saved as part of the mgz volume. When we move the scan from the batch account to the user account, this path is no longer valid. We can fix this by using mri_add_xform_to_header, as per msg02241 on the mailing list (Doug Greve, 27 Jan 2006). What we are wondering is if the mgz header has any other path-dependant information that we would need to update in the scenario such as above, where scan workup and group analysis processing can take place over multiple file locations? +glenn

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer