Sun Jul 2 22:48:07 BST 2006 /Users/bogdand/Free/mine/four/four /Applications/freesurfer/bin//recon-all -i sMS03792-0002-00001-000176-00.img -autorecon1 -s four subjid four setenv SUBJECTS_DIR /Users/bogdand/Free/mine/four FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer Darwin Bogdan-Draganskis-Computer.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 100 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 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: stable3 $ TimeStamp: 06/07/02-21:48:08-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $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@storm.nmr.mgh.harvard.edu (powerpc-apple-darwin8.3.0) on 2005-11-15 at 20:33:57 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:09-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:10-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:11-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:11-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:11-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-21:48:11-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### /Users/bogdand/Free/mine/four/four \n mri_convert /Users/bogdand/Free/mine/four/sMS03792-0002-00001-000176-00.img /Users/bogdand/Free/mine/four/four/mri/orig/001.mgz \n mri_convert /Users/bogdand/Free/mine/four/sMS03792-0002-00001-000176-00.img /Users/bogdand/Free/mine/four/four/mri/orig/001.mgz reading from /Users/bogdand/Free/mine/four/sMS03792-0002-00001-000176-00.img... INFO: reading as a two-file NIFTI INFO: using NIfTI-1 sform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0998334, -0.995004, 0) j_ras = (0, 0, 1) k_ras = (0.995004, 0.0998334, 0) writing to /Users/bogdand/Free/mine/four/four/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jul 2 22:48:57 BST 2006 Found 1 runs /Users/bogdand/Free/mine/four/four/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Users/bogdand/Free/mine/four/four/mri/orig/001.mgz /Users/bogdand/Free/mine/four/four/mri/rawavg.mgz \n /Users/bogdand/Free/mine/four/four \n mri_convert /Users/bogdand/Free/mine/four/four/mri/rawavg.mgz /Users/bogdand/Free/mine/four/four/mri/orig.mgz --conform \n mri_convert /Users/bogdand/Free/mine/four/four/mri/rawavg.mgz /Users/bogdand/Free/mine/four/four/mri/orig.mgz --conform reading from /Users/bogdand/Free/mine/four/four/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0998334, -0.995004, 0) j_ras = (0, 0, 1) k_ras = (0.995004, 0.0998334, 0) Original Data has (1, 1, 1) mm size and (224, 256, 176) 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 /Users/bogdand/Free/mine/four/four/mri/orig.mgz... \n mri_add_xform_to_header -c /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm /Users/bogdand/Free/mine/four/four/mri/orig.mgz /Users/bogdand/Free/mine/four/four/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Jul 2 22:50:27 BST 2006 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 \n /Users/bogdand/Free/mine/four/four/mri /Applications/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 $ Darwin Bogdan-Draganskis-Computer.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc Sun Jul 2 22:50:28 BST 2006 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@storm.nmr.mgh.harvard.edu (powerpc-apple-darwin8.3.0) on 2005-11-15 at 20:33:57 tmpdir is ./tmp.mri_nu_correct.mni.4365 /Users/bogdand/Free/mine/four/four/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4365/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4365/nu0.mnc Can't find the talairach xform '/Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.59496e-10, 0) j_ras = (0, 0, -1) k_ras = (-7.03327e-10, 1, 0) writing to ./tmp.mri_nu_correct.mni.4365/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jul 2 22:51:02 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.4365/nu0.mnc ./tmp.mri_nu_correct.mni.4365/nu1.mnc [bogdand@Bogdan-Draganskis-Computer.local:/Users/bogdand/Free/mine/four/four/mri/] [2006-07-02 22:51:03] running: /Applications/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 /var/tmp/nu_correct_4409/ ./tmp.mri_nu_correct.mni.4365/nu0.mnc ./tmp.mri_nu_correct.mni.4365/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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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: 50 CV of field change: 0.00194078 [bogdand@Bogdan-Draganskis-Computer.local:/Users/bogdand/Free/mine/four/four/mri/] [2006-07-02 22:55:51] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4365/nu0.mnc /var/tmp/nu_correct_4409//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 Sun Jul 2 22:56:44 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.4365/nu1.mnc ./tmp.mri_nu_correct.mni.4365/nu2.mnc [bogdand@Bogdan-Draganskis-Computer.local:/Users/bogdand/Free/mine/four/four/mri/] [2006-07-02 22:56:45] running: /Applications/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 /var/tmp/nu_correct_5054/ ./tmp.mri_nu_correct.mni.4365/nu1.mnc ./tmp.mri_nu_correct.mni.4365/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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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() 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: 50 CV of field change: 0.00145949 [bogdand@Bogdan-Draganskis-Computer.local:/Users/bogdand/Free/mine/four/four/mri/] [2006-07-02 23:01:56] running: /Applications/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4365/nu1.mnc /var/tmp/nu_correct_5054//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.4365/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.4365/nu2.mnc nu.mgz --like orig.mgz Can't find the talairach xform '/Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from ./tmp.mri_nu_correct.mni.4365/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.59497e-10, 0) j_ras = (0, 0, -1) k_ras = (-7.03327e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz Talairach transform /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm writing to nu.mgz... Sun Jul 2 23:04:03 BST 2006 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Sun Jul 2 23:04:03 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n talairach --i nu.mgz --xfm transforms/talairach.auto.xfm \n /Users/bogdand/Free/mine/four/four/mri /Applications/freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ Darwin Bogdan-Draganskis-Computer.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc Sun Jul 2 23:04:03 BST 2006 tmpdir is transforms/tmp.talairach.5726 /Users/bogdand/Free/mine/four/four/mri mri_convert nu.mgz transforms/tmp.talairach.5726/src.mnc mri_convert nu.mgz transforms/tmp.talairach.5726/src.mnc Can't find the talairach xform '/Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from nu.mgz... Talairach transform /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /Users/bogdand/Free/mine/four/four/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.59496e-10, 0) j_ras = (0, 0, -1) k_ras = (-7.03327e-10, 1, 0) writing to transforms/tmp.talairach.5726/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.5726/src.mnc transforms/talairach.auto.xfm Sun Jul 2 23:08:43 BST 2006 talairach done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Intensity Normalization Sun Jul 2 23:08:45 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n WM removal version using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.022 -0.005 0.045 0.609; 0.001 1.007 0.091 3.901; -0.049 -0.100 1.108 -0.429; 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 27 minutes and 32 seconds. white matter peak found at 110 gm peak at 79 (79), valley at 46 (46) csf peak at 40, setting threshold to 66 white matter peak found at 110 gm peak at 78 (78), valley at 45 (45) csf peak at 39, setting threshold to 65 #-------------------------------------------- #@# Skull Stripping Sun Jul 2 23:36:40 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n mri_watershed T1.mgz brainmask.auto.mgz \n ********************************************************* 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 : 313395 Find the largest 110-component...getMemoryUsed works only under Linux current max segment has 293433 voxels removing small segments (less than 1 percent of maxarea). removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 293433 voxels first estimation of the COG coord: x=123 y=98 z=114 r=97 first estimation of the main basin volume: 3866103 voxels global maximum in x=99, y=97, z=68, Imax=255 CSF=14, 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= 1935557 voxels, voxel volume =1.000 = 1935557 mmm3 = 1935.557 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=124,y=103, z=112, r=10663 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=35, TRANSITION=42, GM_MIN=52, GM=78 after analyzing : CSF_MAX=35, TRANSITION=48, GM_MIN=52, GM=55 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* No Rigid alignment: Atlas Mode Off before rotation: sse = 2.77, sigma = 4.45 after rotation: sse = 2.77, sigma = 4.45 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.99, its var is 4.38 before Erosion-Dilatation 1.99% 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...41 iterations mri_strip_skull: done peeling brain Brain Size = 1899964 voxels, voxel volume = 1.000 mm3 = 1899964 mmm3 = 1899.964 cm3 ****************************** Save...done \n cp brainmask.auto.mgz brainmask.mgz \n #------------------------------------------ recon-all finished without error at Sun Jul 2 23:43:26 BST 2006 \n\n New invocation of recon-all \n\n Sun Jul 2 23:51:25 BST 2006 /Users/bogdand/Free/mine/four/four /Applications/freesurfer/bin//recon-all -autorecon2 -s four subjid four setenv SUBJECTS_DIR /Users/bogdand/Free/mine/four FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer Darwin Bogdan-Draganskis-Computer.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 100 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 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: stable3 $ TimeStamp: 06/07/02-22:51:25-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $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@storm.nmr.mgh.harvard.edu (powerpc-apple-darwin8.3.0) on 2005-11-15 at 20:33:57 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:26-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:26-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:26-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:26-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:26-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:27-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:28-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:28-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/07/02-22:51:28-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: bogdand Machine: Bogdan-Draganskis-Computer.local Platform: Darwin PlatformVersion: 8.6.0 CompilerName: GCC CompilerVersion: 40000 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #------------------------------------- #@# EM Registration Sun Jul 2 23:51:28 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n mri_em_register -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (0.9, 16.8, -7.1): log p = -15203.3 Result so far: scale 1.000: max_log_p=-13788.6, old_max_log_p =-15203.3 (thresh=-15188.1) 1.000 0.000 0.000 0.852; 0.000 1.055 0.000 11.197; 0.000 0.000 1.000 -7.102; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-13788.6, old_max_log_p =-13788.6 (thresh=-13774.8) 1.000 0.000 0.000 0.852; 0.000 1.055 0.000 11.197; 0.000 0.000 1.000 -7.102; 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 1.00000 0.00000 0.00000 0.85227; 0.00000 1.05469 0.00000 11.19706; 0.00000 0.00000 1.00000 -7.10227; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.00000 0.00000 0.00000 0.85227; 0.00000 1.05469 0.00000 11.19706; 0.00000 0.00000 1.00000 -7.10227; 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 = 13651.198242, fret = 13651.198242, 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 1.00000 0.00000 0.00000 0.85227; 0.00000 1.05469 0.00000 11.19706; 0.00000 0.00000 1.00000 -7.10227; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.00000 0.00000 0.00000 0.85227; 0.00000 1.05469 0.00000 11.19706; 0.00000 0.00000 1.00000 -7.10227; 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 < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ Note: program considers input volume #1 as the most T1-like using real data threshold=37.8 using (101, 81, 117) as brain centroid... mean wm in atlas = 109, using box (84,67,96) --> (118, 94,138) to find MRI wm before smoothing, mri peak at 100 after smoothing, mri peak at 101, scaling input intensities by 1.078 scaling channel 0 by 1.07793 initial log_p = -44564.4 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 002: -log(p) = 13788.6 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.05, 0.00, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 003: -log(p) = 13690.6 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.05, 0.00, 11.20) ( -0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 004: -log(p) = 13668.6 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.05, 0.00, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 005: -log(p) = 13651.2 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.05, 0.00, 11.20) ( 0.00, 0.00, 1.00, -7.10) outof QuasiNewtonEMA: 007: -log(p) = 13651.2 tol 0.000010 Resulting transform: 1.000 0.000 0.000 0.852; 0.000 1.055 0.000 11.197; 0.000 0.000 1.000 -7.102; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -13788.6 (old=-44564.4) transform before final EM align: 1.000 0.000 0.000 0.852; 0.000 1.055 0.000 11.197; 0.000 0.000 1.000 -7.102; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 006: -log(p) = 1696172.8 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.05, 0.00, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 007: -log(p) = 1691450.2 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( 0.00, 1.06, 0.00, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 008: -log(p) = 1663162.8 after pass:transform: ( 1.01, 0.00, 0.00, 0.85) ( 0.00, 1.06, 0.01, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 009: -log(p) = 1652341.8 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( -0.00, 1.06, 0.01, 11.20) ( 0.00, 0.00, 1.00, -7.10) dfp_em_step_func: 010: -log(p) = 1644857.1 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( -0.00, 1.06, 0.01, 11.20) ( 0.01, 0.01, 1.00, -7.10) dfp_em_step_func: 011: -log(p) = 1634844.9 after pass:transform: ( 1.00, 0.00, 0.00, 0.85) ( -0.01, 1.06, 0.01, 11.20) ( 0.01, 0.00, 1.00, -7.10) outof QuasiNewtonEMA: 013: -log(p) = 1634366.1 tol 0.000000 final transform: 1.006 0.006 0.005 0.852; -0.007 1.063 0.016 11.197; 0.005 0.005 0.999 -7.102; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 16 minutes and 28 seconds. #-------------------------------------- #@# CA Normalize Mon Jul 3 00:07:56 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n mri_ca_normalize -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/Applications/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.006 0.006 0.005 0.852; -0.007 1.063 0.016 11.197; 0.005 0.005 0.999 -7.102; 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=37.8 using (101, 81, 117) as brain centroid... mean wm in atlas = 109, using box (84,67,96) --> (118, 94,138) to find MRI wm before smoothing, mri peak at 100 after smoothing, mri peak at 101, scaling input intensities by 1.078 scaling channel 0 by 1.07793 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (123, 38, 32) --> (189, 148, 198) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 108.0 298 of 674 (44.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (59, 38, 32) --> (123, 148, 198) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 115.0 142 of 820 (17.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (125, 119, 54) --> (171, 158, 108) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 115.0 43 of 108 (39.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (77, 121, 52) --> (123, 158, 108) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 116.0 49 of 85 (57.6%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (105, 109, 88) --> (139, 175, 120) Brain_Stem: limiting intensities to 84.0 --> 103.0 39 of 157 (24.8%) samples deleted using 1844 total control points for intensity normalization... bias field = 1.049 +- 0.096 0 of 1273 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 4 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Mon Jul 3 00:12:11 BST 2006 /Users/bogdand/Free/mine/four/four/mri \n mri_ca_register -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /Applications/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.m3z \n 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 '/Applications/freesurfer/average/RB_all_2006-02-15.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 =74.7677, std = 18.0109 X:57-128; Y:35-152; Z:30-203 gca peak = 0.05652 (116) mri peak = 0.07659 (112) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (99926 voxels, overlap=0.532) aligning Left_Cerebral_White_Matter... source mean =74.6616, std = 17.7766 X:121-193; Y:35-153; Z:29-203 gca peak = 0.05682 (116) mri peak = 0.07177 (114) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (135119 voxels, overlap=0.518) aligning Right_Hippocampus... source mean =80.2596, std = 22.2974 X:84-117; Y:102-140; Z:91-132 gca peak = 0.14805 (66) mri peak = 0.06990 (71) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (2393 voxels, overlap=0.756) aligning Left_Hippocampus... source mean =79.3854, std = 22.1597 X:131-164; Y:100-141; Z:86-131 gca peak = 0.17297 (66) mri peak = 0.06671 (72) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (2579 voxels, overlap=0.972) aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.02103 (79) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.02195 (75) uniform distribution in MR - rejecting arbitrary fit aligning Left_Lateral_Ventricle... source mean =70.9521, std = 37.5843 X:123-160; Y:80-117; Z:69-165 gca peak = 0.05153 (25) mri peak = 0.03167 (77) Left_Lateral_Ventricle (4): linear fit = 3.28 x + 0.0 (5949 voxels, overlap=0.000) aligning Right_Lateral_Ventricle... source mean =70.2791, std = 37.3943 X:89-128; Y:80-119; Z:60-165 gca peak = 0.07557 (30) mri peak = 0.02448 (77) uniform distribution in MR - rejecting arbitrary fit aligning Right_Caudate... source mean =81.0971, std = 33.0028 X:104-125; Y:82-121; Z:111-162 gca peak = 0.07786 (81) mri peak = 0.06604 (88) Right_Caudate (50): linear fit = 1.10 x + 0.0 (1542 voxels, overlap=0.534) aligning Left_Caudate... source mean =84.5467, std = 27.6315 X:125-147; Y:81-123; Z:107-162 gca peak = 0.07814 (81) mri peak = 0.05673 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1664 voxels, overlap=0.635) aligning Left_Cerebellum_Cortex... source mean =56.1599, std = 20.0482 X:121-185; Y:107-176; Z:41-108 gca peak = 0.06033 (63) mri peak = 0.03800 (74) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (44566 voxels, overlap=0.158) aligning Right_Cerebellum_Cortex... source mean =56.3756, std = 20.1165 X:65-128; Y:107-178; Z:41-109 gca peak = 0.05990 (64) mri peak = 0.04174 (79) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (38575 voxels, overlap=0.136) aligning Left_Cerebellum_White_Matter... source mean =84.4595, std = 11.9501 X:123-175; Y:116-163; Z:51-112 gca peak = 0.09299 (92) mri peak = 0.07690 (105) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (7648 voxels, overlap=0.176) aligning Right_Cerebellum_White_Matter... source mean =84.4209, std = 12.2925 X:75-128; Y:118-163; Z:49-113 gca peak = 0.08899 (93) mri peak = 0.07384 (102) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (8984 voxels, overlap=0.308) aligning Left_Amygdala... source mean =70.6541, std = 17.9993 X:131-158; Y:119-142; Z:118-137 gca peak = 0.13911 (71) mri peak = 0.06630 (76) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (672 voxels, overlap=0.380) aligning Right_Amygdala... source mean =71.2297, std = 17.6988 X:90-117; Y:118-142; Z:119-138 gca peak = 0.15703 (65) mri peak = 0.07165 (73) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (889 voxels, overlap=0.612) aligning Left_Thalamus_Proper... source mean =88.8593, std = 24.3831 X:121-152; Y:89-117; Z:93-139 gca peak = 0.06537 (100) mri peak = 0.06063 (97) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (6084 voxels, overlap=0.639) aligning Right_Thalamus_Proper... source mean =86.2989, std = 27.2612 X:99-128; Y:89-117; Z:96-139 gca peak = 0.07019 (99) mri peak = 0.05787 (96) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (6699 v