Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
Hi Gabor,
recon2-cp currently starts *after* the aseg, so you'll need to rerun it from an ealier point than that. Try using -autorecon2 instead.
cheers Bruce On Wed, 3 Mar 2010, Perlaki Gabor wrote:
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks for your help. I've run the recon-all as you told (recon-all -autorecon2 -autorecon3 -subjid C1), but the recon-all exited with errors. I'm sending you the log. Could you help us some more?
Thank you.
Gergely Orsi
New invocation of recon-all
Wed Mar 3 16:00:17 CET 2010 /home/kutato/freesurfer/subjects/C1 /home/kutato/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid C1 subjid C1 setenv SUBJECTS_DIR /home/kutato/freesurfer/subjects FREESURFER_HOME /home/kutato/freesurfer Actual FREESURFER_HOME /home/kutato/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cached Mem: 4020216 2044228 1975988 0 182484 1237240 Swap: 8634360 0 8634360
######################################## program versions used $Id: recon-all,v 1.133.2.38 2009/01/08 19:49:55 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: tkregister2.c,v 1.86.2.7 2009/01/18 19:41:35 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_label.c,v 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ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.5 2009/01/15 01:36:52 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature_stats.c,v 1.28.2.4 2008/10/02 21:42:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #------------------------------------- #@# EM Registration Wed Mar 3 16:00:18 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_em_register -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 initial log_p = -84452.9 ************************************************ First Search limited to translation only. ************************************************
Found translation: (-0.3, -12.2, -22.4): log p = -24312.3 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-24312.3 (thresh=-24288.0) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-12644.5 (thresh=-12631.8) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-12036.9, old_max_log_p =-12644.5 (thresh=-12631.8) 1.067 -0.009 -0.080 4.483; 0.020 1.198 0.188 -64.729; 0.090 -0.169 0.966 -5.663; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-11905.9, old_max_log_p =-12036.9 (thresh=-12024.8) 1.050 -0.009 -0.079 6.394; 0.021 1.195 0.204 -66.521; 0.089 -0.185 0.948 -0.958; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-11904.4, old_max_log_p =-11905.9 (thresh=-11894.0) 1.050 0.011 -0.076 3.377; 0.004 1.214 0.208 -67.391; 0.090 -0.188 0.963 -2.618; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11904.4 (thresh=-11892.5) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11516.2 (thresh=-11504.7) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 11516.2 tol 0.000010 Resulting transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -11516.2 (old=-84452.9) transform before final EM align: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1559944.8 tol 0.000000 final transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta... registration took 38 minutes and 54 seconds. #-------------------------------------- #@# CA Normalize Wed Mar 3 16:39:12 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
reading manually defined control points from /home/kutato/freesurfer/subjects/C1/tmp/control.dat using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 using 244171 sample points... INFO: compute sample coordinates transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 109.0 164 of 520 (31.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 112.0 208 of 519 (40.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 117.0 3 of 14 (21.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 121.0 4 of 21 (19.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 101.0 --> 116.0 6 of 51 (11.8%) samples deleted using 1125 total control points for intensity normalization... bias field = 1.011 +- 0.076 0 of 1450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 171 of 491 (34.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 113.0 132 of 559 (23.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 116.0 16 of 67 (23.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 117.0 10 of 70 (14.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 99.0 --> 113.0 12 of 94 (12.8%) samples deleted using 1281 total control points for intensity normalization... bias field = 0.994 +- 0.088 0 of 1650 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 210 of 555 (37.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 168 of 597 (28.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 113.0 21 of 79 (26.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 113.0 19 of 85 (22.4%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 91.0 --> 106.0 64 of 179 (35.8%) samples deleted using 1495 total control points for intensity normalization... bias field = 0.997 +- 0.082 0 of 1723 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Wed Mar 3 16:40:49 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.27 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.766, neg=0, invalid=766 0001: dt=228.525253, rms=0.731 (4.651%), neg=0, invalid=766 0002: dt=230.826667, rms=0.716 (1.976%), neg=0, invalid=766 0003: dt=131.235955, rms=0.711 (0.775%), neg=0, invalid=766 0004: dt=369.920000, rms=0.705 (0.719%), neg=0, invalid=766 0005: dt=134.901961, rms=0.702 (0.467%), neg=0, invalid=766 0006: dt=295.936000, rms=0.700 (0.338%), neg=0, invalid=766 0007: dt=129.472000, rms=0.698 (0.295%), neg=0, invalid=766 0008: dt=443.904000, rms=0.696 (0.269%), neg=0, invalid=766 0009: dt=142.933333, rms=0.694 (0.331%), neg=0, invalid=766 0010: dt=129.472000, rms=0.693 (0.073%), neg=0, invalid=766 0011: dt=129.472000, rms=0.692 (0.120%), neg=0, invalid=766 0012: dt=129.472000, rms=0.691 (0.183%), neg=0, invalid=766 0013: dt=129.472000, rms=0.689 (0.236%), neg=0, invalid=766 0014: dt=129.472000, rms=0.688 (0.265%), neg=0, invalid=766 0015: dt=129.472000, rms=0.686 (0.290%), neg=0, invalid=766 0016: dt=129.472000, rms=0.684 (0.282%), neg=0, invalid=766 0017: dt=129.472000, rms=0.682 (0.255%), neg=0, invalid=766 0018: dt=129.472000, rms=0.680 (0.239%), neg=0, invalid=766 0019: dt=129.472000, rms=0.679 (0.216%), neg=0, invalid=766 0020: dt=129.472000, rms=0.677 (0.204%), neg=0, invalid=766 0021: dt=129.472000, rms=0.676 (0.193%), neg=0, invalid=766 0022: dt=129.472000, rms=0.675 (0.166%), neg=0, invalid=766 0023: dt=129.472000, rms=0.674 (0.165%), neg=0, invalid=766 0024: dt=129.472000, rms=0.673 (0.171%), neg=0, invalid=766 0025: dt=129.472000, rms=0.672 (0.159%), neg=0, invalid=766 0026: dt=129.472000, rms=0.671 (0.137%), neg=0, invalid=766 0027: dt=129.472000, rms=0.670 (0.106%), neg=0, invalid=766 0028: dt=129.472000, rms=0.669 (0.111%), neg=0, invalid=766 0029: dt=129.472000, rms=0.668 (0.128%), neg=0, invalid=766 0030: dt=129.472000, rms=0.668 (0.109%), neg=0, invalid=766 0031: dt=129.472000, rms=0.667 (0.086%), neg=0, invalid=766 0032: dt=517.888000, rms=0.667 (0.023%), neg=0, invalid=766 0033: dt=517.888000, rms=0.667 (0.014%), neg=0, invalid=766 0034: dt=517.888000, rms=0.667 (-1.199%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0035: dt=129.472000, rms=0.665 (0.222%), neg=0, invalid=766 0036: dt=517.888000, rms=0.664 (0.233%), neg=0, invalid=766 0037: dt=129.472000, rms=0.664 (0.033%), neg=0, invalid=766 0038: dt=129.472000, rms=0.663 (0.026%), neg=0, invalid=766 0039: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0040: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0041: dt=129.472000, rms=0.662 (0.070%), neg=0, invalid=766 0042: dt=129.472000, rms=0.662 (0.085%), neg=0, invalid=766 0043: dt=129.472000, rms=0.661 (0.081%), neg=0, invalid=766 0044: dt=129.472000, rms=0.661 (0.066%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0045: dt=134.243902, rms=0.662 (0.847%), neg=0, invalid=766 0046: dt=136.900662, rms=0.651 (1.582%), neg=0, invalid=766 0047: dt=38.171429, rms=0.648 (0.467%), neg=0, invalid=766 0048: dt=145.152000, rms=0.645 (0.545%), neg=0, invalid=766 0049: dt=115.559395, rms=0.639 (0.880%), neg=0, invalid=766 0050: dt=36.288000, rms=0.638 (0.223%), neg=0, invalid=766 0051: dt=36.288000, rms=0.637 (0.131%), neg=0, invalid=766 0052: dt=36.288000, rms=0.635 (0.241%), neg=0, invalid=766 0053: dt=36.288000, rms=0.633 (0.377%), neg=0, invalid=766 0054: dt=36.288000, rms=0.630 (0.495%), neg=0, invalid=766 0055: dt=36.288000, rms=0.626 (0.531%), neg=0, invalid=766 0056: dt=36.288000, rms=0.623 (0.511%), neg=0, invalid=766 0057: dt=36.288000, rms=0.620 (0.485%), neg=0, invalid=766 0058: dt=36.288000, rms=0.617 (0.438%), neg=0, invalid=766 0059: dt=36.288000, rms=0.615 (0.421%), neg=0, invalid=766 0060: dt=36.288000, rms=0.612 (0.398%), neg=0, invalid=766 0061: dt=36.288000, rms=0.610 (0.353%), neg=0, invalid=766 0062: dt=36.288000, rms=0.609 (0.288%), neg=0, invalid=766 0063: dt=36.288000, rms=0.607 (0.241%), neg=0, invalid=766 0064: dt=36.288000, rms=0.606 (0.222%), neg=0, invalid=766 0065: dt=36.288000, rms=0.604 (0.208%), neg=0, invalid=766 0066: dt=36.288000, rms=0.603 (0.189%), neg=0, invalid=766 0067: dt=36.288000, rms=0.602 (0.167%), neg=0, invalid=766 0068: dt=36.288000, rms=0.601 (0.138%), neg=0, invalid=766 0069: dt=36.288000, rms=0.601 (0.134%), neg=0, invalid=766 0070: dt=36.288000, rms=0.600 (0.136%), neg=0, invalid=766 0071: dt=36.288000, rms=0.599 (0.142%), neg=0, invalid=766 0072: dt=36.288000, rms=0.598 (0.122%), neg=0, invalid=766 0073: dt=36.288000, rms=0.598 (0.110%), neg=0, invalid=766 0074: dt=124.416000, rms=0.597 (0.030%), neg=0, invalid=766 0075: dt=124.416000, rms=0.597 (-0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0076: dt=97.215190, rms=0.596 (0.268%), neg=0, invalid=766 0077: dt=37.647059, rms=0.595 (0.061%), neg=0, invalid=766 0078: dt=37.647059, rms=0.595 (0.033%), neg=0, invalid=766 0079: dt=37.647059, rms=0.595 (0.049%), neg=0, invalid=766 0080: dt=37.647059, rms=0.595 (0.050%), neg=0, invalid=766 0081: dt=37.647059, rms=0.594 (0.046%), neg=0, invalid=766 0082: dt=37.647059, rms=0.594 (0.028%), neg=0, invalid=766 0083: dt=36.288000, rms=0.594 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.59 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0084: dt=4.000000, rms=0.621 (0.022%), neg=0, invalid=766 0085: dt=1.600000, rms=0.621 (0.002%), neg=0, invalid=766 0086: dt=1.600000, rms=0.621 (0.001%), neg=0, invalid=766 0087: dt=1.600000, rms=0.621 (-0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0088: dt=1.600000, rms=0.621 (0.003%), neg=0, invalid=766 0089: dt=0.175000, rms=0.621 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0090: dt=5.778409, rms=0.671 (3.273%), neg=0, invalid=766 0091: dt=4.807692, rms=0.668 (0.356%), neg=0, invalid=766 0092: dt=2.304000, rms=0.668 (0.026%), neg=0, invalid=766 0093: dt=2.304000, rms=0.668 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 0094: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 0095: dt=0.384000, rms=0.717 (0.063%), neg=0, invalid=766 0096: dt=0.514706, rms=0.717 (0.077%), neg=0, invalid=766 0097: dt=1.280000, rms=0.716 (0.178%), neg=0, invalid=766 0098: dt=2.622951, rms=0.712 (0.483%), neg=0, invalid=766 0099: dt=0.448000, rms=0.712 (0.022%), neg=0, invalid=766 0100: dt=0.448000, rms=0.712 (0.029%), neg=0, invalid=766 0101: dt=0.448000, rms=0.711 (0.051%), neg=0, invalid=766 0102: dt=0.448000, rms=0.711 (0.065%), neg=0, invalid=766 0103: dt=0.448000, rms=0.711 (0.069%), neg=0, invalid=766 0104: dt=0.448000, rms=0.710 (0.049%), neg=0, invalid=766 0105: dt=0.448000, rms=0.710 (0.002%), neg=0, invalid=766 0106: dt=1.280000, rms=0.710 (0.013%), neg=0, invalid=766 0107: dt=3.307692, rms=0.709 (0.091%), neg=0, invalid=766 0108: dt=0.384000, rms=0.709 (0.016%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=766 0109: dt=1.024000, rms=0.709 (0.098%), neg=0, invalid=766 0110: dt=0.000000, rms=0.709 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=766 0111: dt=0.768240, rms=0.672 (2.434%), neg=0, invalid=766 0112: dt=0.028000, rms=0.671 (0.144%), neg=0, invalid=766 0113: dt=0.028000, rms=0.671 (-0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.671, neg=0, invalid=766 0114: dt=0.016000, rms=0.670 (0.020%), neg=0, invalid=766 0115: dt=0.000000, rms=0.670 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13848 (32) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, peak = 31), gca=30.6 gca peak = 0.14022 (22) mri peak = 0.14987 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, overlap=0.258) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, peak = 31), gca=31.3 gca peak = 0.24234 (100) mri peak = 0.17616 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.15860 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, overlap=0.633) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.09927 (79) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, peak = 77), gca=77.2 gca peak = 0.29892 (64) mri peak = 0.08177 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, overlap=0.005) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.06542 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.05686 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.02314 (77) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, peak = 80), gca=80.3 gca peak = 0.13270 (63) mri peak = 0.02476 (84) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, peak = 77), gca=77.2 gca peak = 0.15182 (70) mri peak = 0.16579 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, peak = 82), gca=82.2 gca peak = 0.14251 (76) mri peak = 0.22639 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, overlap=0.339) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.02272 (74) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, peak = 80), gca=79.5 gca peak = 0.12723 (61) mri peak = 0.02272 (77) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, peak = 82), gca=82.3 gca peak = 0.22684 (88) mri peak = 0.06491 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, peak = 112), gca=112.2 gca peak = 0.21067 (87) mri peak = 0.06839 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, peak = 109), gca=108.8 gca peak = 0.25455 (62) mri peak = 0.16005 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, peak = 78), gca=77.5 gca peak = 0.39668 (62) mri peak = 0.19364 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.08041 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, overlap=0.801) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.08539 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, overlap=0.548) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, peak = 98), gca=97.9 gca peak = 0.13716 (82) mri peak = 0.09766 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, overlap=0.375) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, peak = 92), gca=92.2 gca peak = 0.15214 (84) mri peak = 0.10719 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, overlap=0.371) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.08349 (101) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, overlap=0.001) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, peak = 102), gca=102.0 gca peak = 0.11809 (92) mri peak = 0.09947 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07866 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.19514 (33) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, overlap=0.860) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, peak = 32), gca=32.4 gca peak = 0.13542 (27) mri peak = 0.12763 (32) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, peak = 34), gca=34.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.22 x + 0.0 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... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0116: dt=108.542373, rms=0.671 (3.115%), neg=0, invalid=766 0117: dt=247.972125, rms=0.664 (1.098%), neg=0, invalid=766 0118: dt=192.927536, rms=0.659 (0.715%), neg=0, invalid=766 0119: dt=87.482014, rms=0.657 (0.292%), neg=0, invalid=766 0120: dt=517.888000, rms=0.653 (0.661%), neg=0, invalid=766 0121: dt=77.748148, rms=0.651 (0.220%), neg=0, invalid=766 0122: dt=2071.552000, rms=0.643 (1.306%), neg=0, invalid=766 0123: dt=71.896869, rms=0.640 (0.383%), neg=0, invalid=766 0124: dt=129.472000, rms=0.640 (0.109%), neg=0, invalid=766 0125: dt=517.888000, rms=0.637 (0.376%), neg=0, invalid=766 0126: dt=73.984000, rms=0.637 (0.062%), neg=0, invalid=766 0127: dt=887.808000, rms=0.635 (0.288%), neg=0, invalid=766 0128: dt=129.472000, rms=0.634 (0.235%), neg=0, invalid=766 0129: dt=517.888000, rms=0.633 (0.150%), neg=0, invalid=766 0130: dt=129.472000, rms=0.632 (0.119%), neg=0, invalid=766 0131: dt=295.936000, rms=0.631 (0.082%), neg=0, invalid=766 0132: dt=129.472000, rms=0.631 (0.085%), neg=0, invalid=766 0133: dt=221.952000, rms=0.630 (0.065%), neg=0, invalid=766 0134: dt=129.472000, rms=0.630 (0.073%), neg=0, invalid=766 0135: dt=295.936000, rms=0.630 (0.058%), neg=0, invalid=766 0136: dt=129.472000, rms=0.629 (0.094%), neg=0, invalid=766 0137: dt=110.976000, rms=0.629 (0.022%), neg=0, invalid=766 0138: dt=110.976000, rms=0.629 (0.053%), neg=0, invalid=766 0139: dt=110.976000, rms=0.628 (0.073%), neg=0, invalid=766 0140: dt=110.976000, rms=0.628 (0.081%), neg=0, invalid=766 0141: dt=110.976000, rms=0.627 (0.103%), neg=0, invalid=766 0142: dt=110.976000, rms=0.626 (0.149%), neg=0, invalid=766 0143: dt=110.976000, rms=0.625 (0.151%), neg=0, invalid=766 0144: dt=110.976000, rms=0.624 (0.152%), neg=0, invalid=766 0145: dt=110.976000, rms=0.623 (0.156%), neg=0, invalid=766 0146: dt=110.976000, rms=0.622 (0.160%), neg=0, invalid=766 0147: dt=110.976000, rms=0.621 (0.164%), neg=0, invalid=766 0148: dt=110.976000, rms=0.620 (0.157%), neg=0, invalid=766 0149: dt=110.976000, rms=0.619 (0.155%), neg=0, invalid=766 0150: dt=110.976000, rms=0.618 (0.154%), neg=0, invalid=766 0151: dt=110.976000, rms=0.617 (0.144%), neg=0, invalid=766 0152: dt=110.976000, rms=0.617 (0.122%), neg=0, invalid=766 0153: dt=110.976000, rms=0.616 (0.134%), neg=0, invalid=766 0154: dt=110.976000, rms=0.615 (0.147%), neg=0, invalid=766 0155: dt=110.976000, rms=0.614 (0.136%), neg=0, invalid=766 0156: dt=110.976000, rms=0.613 (0.119%), neg=0, invalid=766 0157: dt=110.976000, rms=0.613 (0.094%), neg=0, invalid=766 0158: dt=110.976000, rms=0.612 (0.112%), neg=0, invalid=766 0159: dt=110.976000, rms=0.611 (0.119%), neg=0, invalid=766 0160: dt=110.976000, rms=0.611 (0.098%), neg=0, invalid=766 0161: dt=110.976000, rms=0.610 (0.070%), neg=0, invalid=766 0162: dt=110.976000, rms=0.610 (0.093%), neg=0, invalid=766 0163: dt=110.976000, rms=0.609 (0.101%), neg=0, invalid=766 0164: dt=110.976000, rms=0.609 (0.086%), neg=0, invalid=766 0165: dt=110.976000, rms=0.608 (0.069%), neg=0, invalid=766 0166: dt=110.976000, rms=0.608 (0.081%), neg=0, invalid=766 0167: dt=110.976000, rms=0.607 (0.080%), neg=0, invalid=766 0168: dt=110.976000, rms=0.607 (0.067%), neg=0, invalid=766 0169: dt=110.976000, rms=0.606 (0.054%), neg=0, invalid=766 0170: dt=110.976000, rms=0.606 (0.060%), neg=0, invalid=766 0171: dt=110.976000, rms=0.606 (0.064%), neg=0, invalid=766 0172: dt=110.976000, rms=0.605 (0.066%), neg=0, invalid=766 0173: dt=110.976000, rms=0.605 (0.054%), neg=0, invalid=766 0174: dt=110.976000, rms=0.605 (0.053%), neg=0, invalid=766 0175: dt=110.976000, rms=0.604 (0.052%), neg=0, invalid=766 0176: dt=110.976000, rms=0.604 (0.048%), neg=0, invalid=766 0177: dt=110.976000, rms=0.604 (0.045%), neg=0, invalid=766 0178: dt=110.976000, rms=0.604 (0.043%), neg=0, invalid=766 0179: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=766 0180: dt=110.976000, rms=0.603 (0.050%), neg=0, invalid=766 0181: dt=110.976000, rms=0.603 (0.047%), neg=0, invalid=766 0182: dt=110.976000, rms=0.602 (0.035%), neg=0, invalid=766 0183: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=766 0184: dt=110.976000, rms=0.602 (0.040%), neg=0, invalid=766 0185: dt=110.976000, rms=0.602 (0.037%), neg=0, invalid=766 0186: dt=110.976000, rms=0.602 (0.033%), neg=0, invalid=766 0187: dt=110.976000, rms=0.601 (0.037%), neg=0, invalid=766 0188: dt=110.976000, rms=0.601 (0.030%), neg=0, invalid=766 0189: dt=110.976000, rms=0.601 (0.035%), neg=0, invalid=766 0190: dt=110.976000, rms=0.601 (0.040%), neg=0, invalid=766 0191: dt=110.976000, rms=0.601 (0.031%), neg=0, invalid=766 0192: dt=110.976000, rms=0.600 (0.027%), neg=0, invalid=766 0193: dt=110.976000, rms=0.600 (0.038%), neg=0, invalid=766 0194: dt=110.976000, rms=0.600 (0.035%), neg=0, invalid=766 0195: dt=110.976000, rms=0.600 (0.023%), neg=0, invalid=766 0196: dt=110.976000, rms=0.600 (0.028%), neg=0, invalid=766 0197: dt=110.976000, rms=0.599 (0.032%), neg=0, invalid=766 0198: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0199: dt=110.976000, rms=0.599 (0.027%), neg=0, invalid=766 0200: dt=110.976000, rms=0.599 (0.026%), neg=0, invalid=766 0201: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0202: dt=110.976000, rms=0.599 (0.028%), neg=0, invalid=766 0203: dt=110.976000, rms=0.598 (0.022%), neg=0, invalid=766 0204: dt=110.976000, rms=0.598 (0.032%), neg=0, invalid=766 0205: dt=110.976000, rms=0.598 (0.028%), neg=0, invalid=766 0206: dt=110.976000, rms=0.598 (0.021%), neg=0, invalid=766 0207: dt=110.976000, rms=0.598 (0.023%), neg=0, invalid=766 0208: dt=110.976000, rms=0.598 (0.024%), neg=0, invalid=766 0209: dt=110.976000, rms=0.598 (0.025%), neg=0, invalid=766 0210: dt=110.976000, rms=0.597 (0.020%), neg=0, invalid=766 0211: dt=221.952000, rms=0.597 (0.001%), neg=0, invalid=766 0212: dt=221.952000, rms=0.597 (0.014%), neg=0, invalid=766 0213: dt=221.952000, rms=0.597 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0214: dt=221.952000, rms=0.597 (0.077%), neg=0, invalid=766 0215: dt=443.904000, rms=0.596 (0.152%), neg=0, invalid=766 0216: dt=32.368000, rms=0.596 (0.018%), neg=0, invalid=766 0217: dt=32.368000, rms=0.596 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 0218: dt=112.375587, rms=0.596 (0.426%), neg=0, invalid=766 0219: dt=67.729134, rms=0.592 (0.773%), neg=0, invalid=766 0220: dt=31.104000, rms=0.590 (0.211%), neg=0, invalid=766 0221: dt=580.608000, rms=0.577 (2.307%), neg=0, invalid=766 0222: dt=64.000000, rms=0.574 (0.535%), neg=0, invalid=766 0223: dt=25.920000, rms=0.573 (0.091%), neg=0, invalid=766 0224: dt=331.776000, rms=0.571 (0.410%), neg=0, invalid=766 0225: dt=50.070588, rms=0.568 (0.559%), neg=0, invalid=766 0226: dt=20.736000, rms=0.567 (0.042%), neg=0, invalid=766 0227: dt=20.736000, rms=0.567 (0.035%), neg=0, invalid=766 0228: dt=20.736000, rms=0.567 (0.064%), neg=0, invalid=766 0229: dt=20.736000, rms=0.566 (0.111%), neg=0, invalid=766 0230: dt=20.736000, rms=0.565 (0.159%), neg=0, invalid=766 0231: dt=20.736000, rms=0.564 (0.176%), neg=0, invalid=766 0232: dt=20.736000, rms=0.563 (0.180%), neg=0, invalid=766 0233: dt=20.736000, rms=0.562 (0.180%), neg=0, invalid=766 0234: dt=20.736000, rms=0.561 (0.186%), neg=0, invalid=766 0235: dt=20.736000, rms=0.560 (0.201%), neg=0, invalid=766 0236: dt=20.736000, rms=0.559 (0.226%), neg=0, invalid=766 0237: dt=20.736000, rms=0.558 (0.230%), neg=0, invalid=766 0238: dt=20.736000, rms=0.556 (0.228%), neg=0, invalid=766 0239: dt=20.736000, rms=0.555 (0.216%), neg=0, invalid=766 0240: dt=20.736000, rms=0.554 (0.199%), neg=0, invalid=766 0241: dt=20.736000, rms=0.553 (0.192%), neg=0, invalid=766 0242: dt=20.736000, rms=0.552 (0.199%), neg=0, invalid=766 0243: dt=20.736000, rms=0.551 (0.198%), neg=0, invalid=766 0244: dt=20.736000, rms=0.550 (0.186%), neg=0, invalid=766 0245: dt=20.736000, rms=0.549 (0.175%), neg=0, invalid=766 0246: dt=20.736000, rms=0.548 (0.168%), neg=0, invalid=766 0247: dt=20.736000, rms=0.547 (0.160%), neg=0, invalid=766 0248: dt=20.736000, rms=0.546 (0.158%), neg=0, invalid=766 0249: dt=20.736000, rms=0.545 (0.159%), neg=0, invalid=766 0250: dt=20.736000, rms=0.544 (0.150%), neg=0, invalid=766 0251: dt=20.736000, rms=0.544 (0.138%), neg=0, invalid=766 0252: dt=20.736000, rms=0.543 (0.131%), neg=0, invalid=766 0253: dt=20.736000, rms=0.542 (0.127%), neg=0, invalid=766 0254: dt=20.736000, rms=0.542 (0.119%), neg=0, invalid=766 0255: dt=20.736000, rms=0.541 (0.117%), neg=0, invalid=766 0256: dt=20.736000, rms=0.540 (0.117%), neg=0, invalid=766 0257: dt=20.736000, rms=0.540 (0.109%), neg=0, invalid=766 0258: dt=20.736000, rms=0.539 (0.104%), neg=0, invalid=766 0259: dt=20.736000, rms=0.539 (0.098%), neg=0, invalid=766 0260: dt=20.736000, rms=0.538 (0.095%), neg=0, invalid=766 0261: dt=20.736000, rms=0.538 (0.093%), neg=0, invalid=766 0262: dt=20.736000, rms=0.537 (0.087%), neg=0, invalid=766 0263: dt=20.736000, rms=0.537 (0.081%), neg=0, invalid=766 0264: dt=20.736000, rms=0.536 (0.076%), neg=0, invalid=766 0265: dt=20.736000, rms=0.536 (0.075%), neg=0, invalid=766 0266: dt=20.736000, rms=0.535 (0.074%), neg=0, invalid=766 0267: dt=20.736000, rms=0.535 (0.073%), neg=0, invalid=766 0268: dt=20.736000, rms=0.535 (0.071%), neg=0, invalid=766 0269: dt=20.736000, rms=0.534 (0.067%), neg=0, invalid=766 0270: dt=20.736000, rms=0.534 (0.068%), neg=0, invalid=766 0271: dt=20.736000, rms=0.534 (0.066%), neg=0, invalid=766 0272: dt=20.736000, rms=0.533 (0.063%), neg=0, invalid=766 0273: dt=20.736000, rms=0.533 (0.058%), neg=0, invalid=766 0274: dt=20.736000, rms=0.533 (0.062%), neg=0, invalid=766 0275: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0276: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0277: dt=20.736000, rms=0.532 (0.059%), neg=0, invalid=766 0278: dt=20.736000, rms=0.531 (0.054%), neg=0, invalid=766 0279: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0280: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0281: dt=20.736000, rms=0.531 (0.045%), neg=0, invalid=766 0282: dt=20.736000, rms=0.530 (0.047%), neg=0, invalid=766 0283: dt=20.736000, rms=0.530 (0.050%), neg=0, invalid=766 0284: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0285: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0286: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0287: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0288: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0289: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0290: dt=20.736000, rms=0.529 (0.037%), neg=0, invalid=766 0291: dt=20.736000, rms=0.528 (0.037%), neg=0, invalid=766 0292: dt=20.736000, rms=0.528 (0.033%), neg=0, invalid=766 0293: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0294: dt=20.736000, rms=0.528 (0.035%), neg=0, invalid=766 0295: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0296: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0297: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0298: dt=20.736000, rms=0.527 (0.030%), neg=0, invalid=766 0299: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0300: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0301: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0302: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0303: dt=20.736000, rms=0.526 (0.031%), neg=0, invalid=766 0304: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0305: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0306: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0307: dt=20.736000, rms=0.526 (0.024%), neg=0, invalid=766 0308: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0309: dt=20.736000, rms=0.526 (0.027%), neg=0, invalid=766 0310: dt=20.736000, rms=0.526 (0.023%), neg=0, invalid=766 0311: dt=20.736000, rms=0.525 (0.026%), neg=0, invalid=766 0312: dt=20.736000, rms=0.525 (0.022%), neg=0, invalid=766 0313: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0314: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0315: dt=580.608000, rms=0.525 (0.040%), neg=0, invalid=766 0316: dt=31.104000, rms=0.525 (0.015%), neg=0, invalid=766 0317: dt=31.104000, rms=0.525 (0.007%), neg=0, invalid=766 0318: dt=31.104000, rms=0.525 (0.004%), neg=0, invalid=766 0319: dt=31.104000, rms=0.525 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=766 0320: dt=136.072072, rms=0.523 (0.371%), neg=0, invalid=766 0321: dt=36.288000, rms=0.522 (0.046%), neg=0, invalid=766 0322: dt=36.288000, rms=0.522 (0.054%), neg=0, invalid=766 0323: dt=36.288000, rms=0.522 (0.039%), neg=0, invalid=766 0324: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=766 0325: dt=36.288000, rms=0.522 (0.058%), neg=0, invalid=766 0326: dt=36.288000, rms=0.521 (0.085%), neg=0, invalid=766 0327: dt=36.288000, rms=0.521 (0.066%), neg=0, invalid=766 0328: dt=36.288000, rms=0.521 (0.044%), neg=0, invalid=766 0329: dt=36.288000, rms=0.520 (0.041%), neg=0, invalid=766 0330: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0331: dt=36.288000, rms=0.520 (0.046%), neg=0, invalid=766 0332: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0333: dt=36.288000, rms=0.519 (0.056%), neg=0, invalid=766 0334: dt=36.288000, rms=0.519 (0.055%), neg=0, invalid=766 0335: dt=36.288000, rms=0.519 (0.053%), neg=0, invalid=766 0336: dt=36.288000, rms=0.518 (0.052%), neg=0, invalid=766 0337: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0338: dt=36.288000, rms=0.518 (0.042%), neg=0, invalid=766 0339: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0340: dt=36.288000, rms=0.518 (0.047%), neg=0, invalid=766 0341: dt=36.288000, rms=0.517 (0.046%), neg=0, invalid=766 0342: dt=36.288000, rms=0.517 (0.035%), neg=0, invalid=766 0343: dt=36.288000, rms=0.517 (0.036%), neg=0, invalid=766 0344: dt=36.288000, rms=0.517 (0.033%), neg=0, invalid=766 0345: dt=36.288000, rms=0.517 (0.031%), neg=0, invalid=766 0346: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0347: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0348: dt=36.288000, rms=0.516 (0.038%), neg=0, invalid=766 0349: dt=36.288000, rms=0.516 (0.033%), neg=0, invalid=766 0350: dt=36.288000, rms=0.516 (0.034%), neg=0, invalid=766 0351: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0352: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0353: dt=36.288000, rms=0.515 (0.027%), neg=0, invalid=766 0354: dt=36.288000, rms=0.515 (0.032%), neg=0, invalid=766 0355: dt=36.288000, rms=0.515 (0.036%), neg=0, invalid=766 0356: dt=36.288000, rms=0.515 (0.031%), neg=0, invalid=766 0357: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0358: dt=36.288000, rms=0.515 (0.022%), neg=0, invalid=766 0359: dt=36.288000, rms=0.514 (0.028%), neg=0, invalid=766 0360: dt=36.288000, rms=0.514 (0.026%), neg=0, invalid=766 0361: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0362: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0363: dt=36.288000, rms=0.514 (0.024%), neg=0, invalid=766 0364: dt=124.416000, rms=0.514 (0.012%), neg=0, invalid=766 0365: dt=124.416000, rms=0.514 (-0.159%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 0366: dt=20.227979, rms=0.525 (0.130%), neg=0, invalid=766 0367: dt=31.326316, rms=0.524 (0.190%), neg=0, invalid=766 0368: dt=12.972973, rms=0.523 (0.137%), neg=0, invalid=766 0369: dt=59.508772, rms=0.522 (0.302%), neg=0, invalid=766 0370: dt=13.479452, rms=0.521 (0.263%), neg=0, invalid=766 0371: dt=179.200000, rms=0.517 (0.721%), neg=0, invalid=766 0372: dt=24.457539, rms=0.514 (0.537%), neg=0, invalid=766 0373: dt=21.157025, rms=0.513 (0.170%), neg=0, invalid=766 0374: dt=38.303030, rms=0.512 (0.170%), neg=0, invalid=766 0375: dt=11.200000, rms=0.512 (0.098%), neg=0, invalid=766 0376: dt=44.800000, rms=0.511 (0.160%), neg=0, invalid=766 0377: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=766 0378: dt=38.400000, rms=0.510 (0.132%), neg=0, invalid=766 0379: dt=11.200000, rms=0.509 (0.068%), neg=0, invalid=766 0380: dt=25.600000, rms=0.509 (0.079%), neg=0, invalid=766 0381: dt=11.200000, rms=0.509 (0.048%), neg=0, invalid=766 0382: dt=11.200000, rms=0.509 (0.055%), neg=0, invalid=766 0383: dt=11.200000, rms=0.508 (0.066%), neg=0, invalid=766 0384: dt=11.200000, rms=0.508 (0.092%), neg=0, invalid=766 0385: dt=11.200000, rms=0.507 (0.109%), neg=0, invalid=766 0386: dt=11.200000, rms=0.506 (0.139%), neg=0, invalid=766 0387: dt=11.200000, rms=0.506 (0.146%), neg=0, invalid=766 0388: dt=11.200000, rms=0.505 (0.155%), neg=0, invalid=766 0389: dt=11.200000, rms=0.504 (0.151%), neg=0, invalid=766 0390: dt=11.200000, rms=0.503 (0.168%), neg=0, invalid=766 0391: dt=11.200000, rms=0.503 (0.165%), neg=0, invalid=766 0392: dt=11.200000, rms=0.502 (0.158%), neg=0, invalid=766 0393: dt=11.200000, rms=0.501 (0.146%), neg=0, invalid=766 0394: dt=11.200000, rms=0.500 (0.133%), neg=0, invalid=766 0395: dt=11.200000, rms=0.500 (0.140%), neg=0, invalid=766 0396: dt=11.200000, rms=0.499 (0.132%), neg=0, invalid=766 0397: dt=11.200000, rms=0.498 (0.118%), neg=0, invalid=766 0398: dt=11.200000, rms=0.498 (0.112%), neg=0, invalid=766 0399: dt=11.200000, rms=0.497 (0.116%), neg=0, invalid=766 0400: dt=11.200000, rms=0.497 (0.105%), neg=0, invalid=766 0401: dt=11.200000, rms=0.496 (0.097%), neg=0, invalid=766 0402: dt=11.200000, rms=0.496 (0.083%), neg=0, invalid=766 0403: dt=11.200000, rms=0.495 (0.089%), neg=0, invalid=766 0404: dt=11.200000, rms=0.495 (0.084%), neg=0, invalid=766 0405: dt=11.200000, rms=0.495 (0.074%), neg=0, invalid=766 0406: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0407: dt=11.200000, rms=0.494 (0.060%), neg=0, invalid=766 0408: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0409: dt=11.200000, rms=0.493 (0.054%), neg=0, invalid=766 0410: dt=11.200000, rms=0.493 (0.053%), neg=0, invalid=766 0411: dt=11.200000, rms=0.493 (0.040%), neg=0, invalid=766 0412: dt=11.200000, rms=0.493 (0.051%), neg=0, invalid=766 0413: dt=11.200000, rms=0.493 (0.041%), neg=0, invalid=766 0414: dt=11.200000, rms=0.492 (0.040%), neg=0, invalid=766 0415: dt=11.200000, rms=0.492 (0.035%), neg=0, invalid=766 0416: dt=11.200000, rms=0.492 (0.041%), neg=0, invalid=766 0417: dt=11.200000, rms=0.492 (0.045%), neg=0, invalid=766 0418: dt=11.200000, rms=0.492 (0.031%), neg=0, invalid=766 0419: dt=11.200000, rms=0.491 (0.026%), neg=0, invalid=766 0420: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0421: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0422: dt=11.200000, rms=0.491 (0.023%), neg=0, invalid=766 0423: dt=11.200000, rms=0.491 (0.019%), neg=0, invalid=766 0424: dt=25.600000, rms=0.491 (0.018%), neg=0, invalid=766 0425: dt=25.600000, rms=0.491 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=766 0426: dt=28.444444, rms=0.490 (0.167%), neg=0, invalid=766 0427: dt=12.000000, rms=0.490 (0.084%), neg=0, invalid=766 0428: dt=9.600000, rms=0.489 (0.017%), neg=0, invalid=766 0429: dt=9.600000, rms=0.489 (0.022%), neg=0, invalid=766 0430: dt=9.600000, rms=0.489 (0.014%), neg=0, invalid=766 0431: dt=9.600000, rms=0.489 (0.005%), neg=0, invalid=766 0432: dt=25.600000, rms=0.489 (0.013%), neg=0, invalid=766 0433: dt=4.000000, rms=0.489 (0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0434: dt=0.000000, rms=0.519 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0435: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=766 0436: dt=1.963333, rms=0.567 (1.560%), neg=0, invalid=766 0437: dt=0.525000, rms=0.567 (0.074%), neg=0, invalid=766 0438: dt=0.448000, rms=0.567 (0.019%), neg=0, invalid=766 0439: dt=0.448000, rms=0.567 (-0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=766 0440: dt=1.282051, rms=0.566 (0.177%), neg=0, invalid=766 0441: dt=0.448000, rms=0.565 (0.014%), neg=0, invalid=766 0442: dt=0.448000, rms=0.565 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 0443: dt=0.448000, rms=0.502 (2.666%), neg=0, invalid=766 0444: dt=0.448000, rms=0.499 (0.609%), neg=0, invalid=766 0445: dt=0.448000, rms=0.497 (0.408%), neg=0, invalid=766 0446: dt=0.448000, rms=0.495 (0.275%), neg=0, invalid=766 0447: dt=0.448000, rms=0.494 (0.209%), neg=0, invalid=766 0448: dt=0.448000, rms=0.493 (0.162%), neg=0, invalid=766 0449: dt=0.028000, rms=0.493 (0.007%), neg=0, invalid=766 0450: dt=0.028000, rms=0.493 (0.009%), neg=0, invalid=766 0451: dt=0.028000, rms=0.493 (0.015%), neg=0, invalid=766 0452: dt=0.028000, rms=0.493 (0.023%), neg=0, invalid=766 0453: dt=0.028000, rms=0.493 (0.028%), neg=0, invalid=766 0454: dt=0.028000, rms=0.493 (0.031%), neg=0, invalid=766 0455: dt=0.028000, rms=0.493 (0.037%), neg=0, invalid=766 0456: dt=0.028000, rms=0.492 (0.038%), neg=0, invalid=766 0457: dt=0.028000, rms=0.492 (0.039%), neg=0, invalid=766 0458: dt=0.028000, rms=0.492 (0.043%), neg=0, invalid=766 0459: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0460: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0461: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0462: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0463: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0464: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0465: dt=0.028000, rms=0.491 (0.039%), neg=0, invalid=766 0466: dt=0.028000, rms=0.490 (0.039%), neg=0, invalid=766 0467: dt=0.028000, rms=0.490 (0.036%), neg=0, invalid=766 0468: dt=0.028000, rms=0.490 (0.002%), neg=0, invalid=766 0469: dt=0.028000, rms=0.490 (0.004%), neg=0, invalid=766 0470: dt=0.028000, rms=0.490 (0.006%), neg=0, invalid=766 0471: dt=0.028000, rms=0.490 (0.008%), neg=0, invalid=766 0472: dt=0.028000, rms=0.490 (0.007%), neg=0, invalid=766 0473: dt=0.461538, rms=0.490 (0.033%), neg=0, invalid=766 0474: dt=0.024000, rms=0.490 (0.001%), neg=0, invalid=766 0475: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0476: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0477: dt=0.024000, rms=0.490 (0.004%), neg=0, invalid=766 0478: dt=0.024000, rms=0.490 (0.005%), neg=0, invalid=766 0479: dt=0.024000, rms=0.490 (0.006%), neg=0, invalid=766 0480: dt=0.024000, rms=0.490 (0.007%), neg=0, invalid=766 0481: dt=0.024000, rms=0.490 (0.008%), neg=0, invalid=766 0482: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0483: dt=0.024000, rms=0.490 (0.009%), neg=0, invalid=766 0484: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0485: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0486: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0487: dt=0.024000, rms=0.489 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=766 0488: dt=0.384000, rms=0.486 (0.728%), neg=0, invalid=766 0489: dt=0.028000, rms=0.486 (0.009%), neg=0, invalid=766 0490: dt=0.028000, rms=0.486 (0.010%), neg=0, invalid=766 0491: dt=0.028000, rms=0.486 (0.017%), neg=0, invalid=766 0492: dt=0.028000, rms=0.486 (0.024%), neg=0, invalid=766 0493: dt=0.028000, rms=0.485 (0.027%), neg=0, invalid=766 0494: dt=0.028000, rms=0.485 (0.030%), neg=0, invalid=766 0495: dt=0.028000, rms=0.485 (0.029%), neg=0, invalid=766 0496: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=766 0497: dt=0.028000, rms=0.485 (0.026%), neg=0, invalid=766 0498: dt=0.028000, rms=0.485 (0.024%), neg=0, invalid=766 0499: dt=0.028000, rms=0.485 (0.018%), neg=0, invalid=766 0500: dt=0.000000, rms=0.485 (-0.001%), neg=0, invalid=766 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... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 0501: dt=73.984000, rms=0.483 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=766 0502: dt=129.472000, rms=0.482 (0.113%), neg=0, invalid=766 0503: dt=221.952000, rms=0.482 (0.068%), neg=0, invalid=766 0504: dt=129.472000, rms=0.481 (0.056%), neg=0, invalid=766 0505: dt=110.976000, rms=0.481 (0.027%), neg=0, invalid=766 0506: dt=110.976000, rms=0.481 (0.030%), neg=0, invalid=766 0507: dt=110.976000, rms=0.481 (0.041%), neg=0, invalid=766 0508: dt=110.976000, rms=0.481 (0.053%), neg=0, invalid=766 0509: dt=110.976000, rms=0.481 (0.049%), neg=0, invalid=766 0510: dt=110.976000, rms=0.480 (0.059%), neg=0, invalid=766 0511: dt=110.976000, rms=0.480 (0.053%), neg=0, invalid=766 0512: dt=110.976000, rms=0.480 (0.054%), neg=0, invalid=766 0513: dt=110.976000, rms=0.480 (0.049%), neg=0, invalid=766 0514: dt=110.976000, rms=0.479 (0.049%), neg=0, invalid=766 0515: dt=110.976000, rms=0.479 (0.047%), neg=0, invalid=766 0516: dt=110.976000, rms=0.479 (0.044%), neg=0, invalid=766 0517: dt=110.976000, rms=0.479 (0.043%), neg=0, invalid=766 0518: dt=110.976000, rms=0.478 (0.037%), neg=0, invalid=766 0519: dt=110.976000, rms=0.478 (0.036%), neg=0, invalid=766 0520: dt=110.976000, rms=0.478 (0.031%), neg=0, invalid=766 0521: dt=110.976000, rms=0.478 (0.030%), neg=0, invalid=766 0522: dt=110.976000, rms=0.478 (0.028%), neg=0, invalid=766 0523: dt=110.976000, rms=0.478 (0.025%), neg=0, invalid=766 0524: dt=110.976000, rms=0.478 (0.022%), neg=0, invalid=766 0525: dt=443.904000, rms=0.478 (0.005%), neg=0, invalid=766 0526: dt=443.904000, rms=0.478 (-0.062%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 0527: dt=38.588235, rms=0.477 (0.078%), neg=0, invalid=766 0528: dt=103.680000, rms=0.477 (0.118%), neg=0, invalid=766 0529: dt=145.152000, rms=0.475 (0.331%), neg=0, invalid=766 0530: dt=36.288000, rms=0.475 (0.018%), neg=0, invalid=766 0531: dt=36.288000, rms=0.475 (0.035%), neg=0, invalid=766 0532: dt=36.288000, rms=0.475 (0.064%), neg=0, invalid=766 0533: dt=36.288000, rms=0.474 (0.087%), neg=0, invalid=766 0534: dt=36.288000, rms=0.474 (0.100%), neg=0, invalid=766 0535: dt=18.144000, rms=0.474 (0.019%), neg=0, invalid=766 0536: dt=9.072000, rms=0.474 (0.010%), neg=0, invalid=766 0537: dt=6.480000, rms=0.474 (0.007%), neg=0, invalid=766 0538: dt=0.101250, rms=0.474 (0.000%), neg=0, invalid=766 0539: dt=0.025312, rms=0.474 (0.000%), neg=0, invalid=766 0540: dt=0.012656, rms=0.474 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 0541: dt=132.512821, rms=0.471 (0.546%), neg=0, invalid=766 0542: dt=44.800000, rms=0.470 (0.141%), neg=0, invalid=766 0543: dt=103.680000, rms=0.470 (0.116%), neg=0, invalid=766 0544: dt=414.720000, rms=0.468 (0.287%), neg=0, invalid=766 0545: dt=43.000000, rms=0.468 (0.096%), neg=0, invalid=766 0546: dt=36.288000, rms=0.468 (0.019%), neg=0, invalid=766 0547: dt=36.288000, rms=0.468 (0.017%), neg=0, invalid=766 0548: dt=18.144000, rms=0.468 (0.008%), neg=0, invalid=766 0549: dt=9.072000, rms=0.468 (0.004%), neg=0, invalid=766 0550: dt=9.072000, rms=0.468 (0.005%), neg=0, invalid=766 0551: dt=0.567000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 0552: dt=11.200000, rms=0.467 (0.281%), neg=0, invalid=766 0553: dt=0.700000, rms=0.467 (0.016%), neg=0, invalid=766 0554: dt=0.350000, rms=0.467 (0.008%), neg=0, invalid=766 0555: dt=0.175000, rms=0.467 (0.004%), neg=0, invalid=766 0556: dt=0.021875, rms=0.467 (0.000%), neg=0, invalid=766 0557: dt=0.000684, rms=0.467 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0558: dt=44.800000, rms=0.462 (1.098%), neg=0, invalid=766 0559: dt=44.800000, rms=0.459 (0.606%), neg=0, invalid=766 0560: dt=38.400000, rms=0.457 (0.489%), neg=0, invalid=766 0561: dt=44.800000, rms=0.456 (0.222%), neg=0, invalid=766 0562: dt=11.200000, rms=0.455 (0.147%), neg=0, invalid=766 0563: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0564: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0565: dt=0.043750, rms=0.455 (0.000%), neg=0, invalid=766 0566: dt=0.005469, rms=0.455 (0.000%), neg=0, invalid=766 0567: dt=0.000684, rms=0.455 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0568: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0569: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 0570: dt=0.906250, rms=0.465 (0.232%), neg=0, invalid=766 0571: dt=0.448000, rms=0.464 (0.065%), neg=0, invalid=766 0572: dt=0.681818, rms=0.464 (0.070%), neg=0, invalid=766 0573: dt=1.792000, rms=0.464 (0.057%), neg=0, invalid=766 0574: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 0575: dt=0.100000, rms=0.464 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0576: dt=1.536000, rms=0.463 (0.243%), neg=0, invalid=766 0577: dt=0.541667, rms=0.462 (0.043%), neg=0, invalid=766 0578: dt=0.541667, rms=0.462 (0.036%), neg=0, invalid=766 0579: dt=0.541667, rms=0.462 (0.056%), neg=0, invalid=766 0580: dt=0.541667, rms=0.462 (0.018%), neg=0, invalid=766 0581: dt=0.541667, rms=0.462 (0.027%), neg=0, invalid=766 0582: dt=0.541667, rms=0.462 (0.024%), neg=0, invalid=766 0583: dt=0.541667, rms=0.462 (0.010%), neg=0, invalid=766 0584: dt=0.000000, rms=0.462 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 0585: dt=0.140550, rms=0.451 (0.763%), neg=0, invalid=766 0586: dt=0.122596, rms=0.449 (0.477%), neg=0, invalid=766 0587: dt=0.112257, rms=0.448 (0.334%), neg=0, invalid=766 0588: dt=0.112000, rms=0.447 (0.265%), neg=0, invalid=766 0589: dt=0.112000, rms=0.446 (0.214%), neg=0, invalid=766 0590: dt=0.112000, rms=0.445 (0.174%), neg=0, invalid=766 0591: dt=0.112000, rms=0.444 (0.144%), neg=0, invalid=766 0592: dt=0.112000, rms=0.444 (0.120%), neg=0, invalid=766 0593: dt=0.112000, rms=0.443 (0.101%), neg=0, invalid=766 0594: dt=0.112000, rms=0.443 (0.086%), neg=0, invalid=766 0595: dt=0.112000, rms=0.442 (0.074%), neg=0, invalid=766 0596: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0597: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0598: dt=0.028000, rms=0.442 (0.029%), neg=0, invalid=766 0599: dt=0.028000, rms=0.442 (0.040%), neg=0, invalid=766 0600: dt=0.028000, rms=0.442 (0.049%), neg=0, invalid=766 0601: dt=0.028000, rms=0.442 (0.011%), neg=0, invalid=766 0602: dt=0.028000, rms=0.442 (0.021%), neg=0, invalid=766 0603: dt=0.028000, rms=0.442 (0.030%), neg=0, invalid=766 0604: dt=0.028000, rms=0.441 (0.037%), neg=0, invalid=766 0605: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0606: dt=0.028000, rms=0.441 (0.045%), neg=0, invalid=766 0607: dt=0.028000, rms=0.441 (0.007%), neg=0, invalid=766 0608: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0609: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0610: dt=0.112000, rms=0.441 (0.025%), neg=0, invalid=766 0611: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0612: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0613: dt=0.028000, rms=0.441 (0.011%), neg=0, invalid=766 0614: dt=0.028000, rms=0.441 (0.015%), neg=0, invalid=766 0615: dt=0.028000, rms=0.441 (0.018%), neg=0, invalid=766 0616: dt=0.028000, rms=0.440 (0.021%), neg=0, invalid=766 0617: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 0618: dt=0.028000, rms=0.440 (0.008%), neg=0, invalid=766 0619: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=766 0620: dt=0.028000, rms=0.440 (0.058%), neg=0, invalid=766 0621: dt=0.028000, rms=0.440 (0.054%), neg=0, invalid=766 0622: dt=0.024000, rms=0.440 (0.043%), neg=0, invalid=766 0623: dt=0.024000, rms=0.439 (0.041%), neg=0, invalid=766 0624: dt=0.024000, rms=0.439 (0.075%), neg=0, invalid=766 0625: dt=0.024000, rms=0.439 (0.035%), neg=0, invalid=766 0626: dt=0.024000, rms=0.439 (0.064%), neg=0, invalid=766 0627: dt=0.024000, rms=0.438 (0.086%), neg=0, invalid=766 0628: dt=0.024000, rms=0.438 (0.101%), neg=0, invalid=766 0629: dt=0.024000, rms=0.437 (0.108%), neg=0, invalid=766 0630: dt=0.024000, rms=0.437 (0.109%), neg=0, invalid=766 0631: dt=0.024000, rms=0.436 (0.104%), neg=0, invalid=766 0632: dt=0.024000, rms=0.436 (0.095%), neg=0, invalid=766 0633: dt=0.024000, rms=0.436 (0.082%), neg=0, invalid=766 0634: dt=0.024000, rms=0.435 (0.068%), neg=0, invalid=766 0635: dt=0.024000, rms=0.435 (0.053%), neg=0, invalid=766 0636: dt=0.024000, rms=0.435 (0.038%), neg=0, invalid=766 0637: dt=0.024000, rms=0.435 (0.023%), neg=0, invalid=766 0638: dt=0.024000, rms=0.435 (0.009%), neg=0, invalid=766 0639: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 4 hours, 9 minutes and 13 seconds. #-------------------------------------- #@# CA Reg Inv Wed Mar 3 20:50:02 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Mar 3 20:51:02 CET 2010
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11104963 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA Wed Mar 3 20:52:16 CET 2010
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.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 '/home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (45, 52, 28) --> (207, 202, 237) using (99, 102, 133) as brain centroid... mean wm in atlas = 126, using box (79,84,107) --> (118, 120,158) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 140, scaling input intensities by 0.900 scaling channel 0 by 0.9 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-17103.0 (thresh=-17085.9) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-14667.9 (thresh=-14653.3) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-14488.4, old_max_log_p =-14667.9 (thresh=-14653.3) 1.036 -0.063 -0.081 14.725; 0.070 1.213 0.222 -79.106; 0.083 -0.208 0.964 -0.991; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14488.4 (thresh=-14473.9) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14436.8 (thresh=-14422.4) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14436.8 (thresh=-14422.4) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14336.6 (thresh=-14322.3) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 14336.6 tol 0.000010 Resulting transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -14336.6 (old=-17103.0) transform before final EM align: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1833208.1 tol 0.000000 final transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta... registration took 49 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Wed Mar 3 21:42:15 CET 2010
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
$Id: mri_seg_diff.c,v 1.3.2.1 2008/09/03 22:02:00 nicks Exp $ cwd /home/kutato/freesurfer/subjects/C1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname localhost.localdomain machine x86_64 user kutato Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmenations No difference found.
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /home/kutato/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /home/kutato/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, overlap=0.688) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, peak = 32), gca=32.4 gca peak = 0.14982 (20) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, overlap=0.231) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, peak = 28), gca=28.5 gca peak = 0.28003 (97) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, peak = 102), gca=101.8 gca peak = 0.18160 (96) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, overlap=0.407) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, peak = 78), gca=77.5 gca peak = 0.32745 (63) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, peak = 77), gca=77.2 gca peak = 0.08597 (105) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, overlap=0.045) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, peak = 80), gca=80.3 gca peak = 0.08598 (64) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, overlap=0.074) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, peak = 85), gca=85.2 gca peak = 0.18227 (75) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, overlap=0.228) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, peak = 84), gca=84.4 gca peak = 0.10629 (62) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, peak = 85), gca=85.2 gca peak = 0.11668 (59) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, peak = 83), gca=82.6 gca peak = 0.17849 (88) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, peak = 112), gca=112.2 gca peak = 0.16819 (86) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, peak = 108), gca=107.5 gca peak = 0.41688 (64) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, peak = 80), gca=80.0 gca peak = 0.42394 (62) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, peak = 81), gca=80.6 gca peak = 0.10041 (96) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, overlap=0.774) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, overlap=0.443) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, overlap=0.331) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, peak = 91), gca=91.1 gca peak = 0.09624 (82) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, overlap=0.394) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, overlap=0.000) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, peak = 103), gca=103.4 gca peak = 0.12757 (95) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, overlap=0.525) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, overlap=0.902) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, peak = 32), gca=32.4 gca peak = 0.26069 (23) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, overlap=0.240) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.23 x + 0.0 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14396 (33) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, overlap=0.871) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, peak = 31), gca=31.4 gca peak = 0.13467 (29) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, overlap=0.673) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, peak = 31), gca=31.2 gca peak = 0.27948 (102) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, peak = 102), gca=102.0 gca peak = 0.18507 (101) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, peak = 101), gca=101.0 gca peak = 0.21463 (78) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, peak = 76), gca=76.1 gca peak = 0.27122 (77) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 77), gca=77.0 gca peak = 0.08007 (112) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, overlap=0.810) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, peak = 112), gca=112.0 gca peak = 0.08789 (111) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, overlap=0.795) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, peak = 114), gca=113.8 gca peak = 0.06240 (80) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, overlap=0.591) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, peak = 78), gca=78.0 gca peak = 0.07094 (77) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, overlap=0.711) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, peak = 75), gca=75.1 gca peak = 0.23769 (85) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, peak = 85), gca=85.0 gca peak = 0.13104 (84) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, overlap=0.845) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, peak = 86), gca=86.1 gca peak = 0.08141 (85) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, overlap=0.690) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, peak = 83), gca=82.9 gca peak = 0.09212 (83) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, overlap=0.736) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, peak = 83), gca=83.0 gca peak = 0.14004 (112) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, overlap=0.965) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, peak = 112), gca=112.0 gca peak = 0.13912 (108) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, peak = 108), gca=108.0 gca peak = 0.30905 (79) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 81), gca=81.0 gca peak = 0.37870 (81) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, peak = 79), gca=79.0 gca peak = 0.10116 (99) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, overlap=0.963) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, peak = 99), gca=99.0 gca peak = 0.09774 (97) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, overlap=0.918) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, peak = 97), gca=97.0 gca peak = 0.08941 (98) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, peak = 98), gca=98.0 gca peak = 0.08263 (85) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, overlap=0.828) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, peak = 85), gca=85.0 gca peak = 0.06255 (104) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, overlap=0.638) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, peak = 104), gca=104.0 gca peak = 0.14189 (104) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, overlap=0.808) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, peak = 104), gca=104.0 gca peak = 0.16147 (99) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, peak = 99), gca=99.0 gca peak = 0.22647 (34) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, overlap=0.851) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, peak = 33), gca=33.2 gca peak = 0.16050 (32) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, overlap=0.781) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, peak = 32), gca=32.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26758 (43) gca peak CSF = 0.17739 (47) gca peak Left_Accumbens_area = 0.36131 (79) gca peak Left_undetermined = 0.95107 (38) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.22906 (40) gca peak Right_Accumbens_area = 0.27742 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.12959 (48) gca peak Fifth_Ventricle = 0.50102 (51) gca peak WM_hypointensities = 0.15008 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34132 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 33062 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 306 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77084 changed. image ll: -2.213, PF=1.000 pass 2: 12120 changed. image ll: -2.211, PF=1.000 pass 3: 4101 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 30 minutes and 38 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz C1
reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /home/kutato/freesurfer/subjects/C1/mri/aseg.auto_noCCseg.mgz reading norm from /home/kutato/freesurfer/subjects/C1/mri/norm.mgz 44494 voxels in left wm, 85128 in right wm, xrange [115, 131] global minimum found at slice 125.0, rotations (-3.75, -0.25) final transformation (x=125.0, yr=-3.750, zr=-0.250): 0.998 0.004 -0.065 11.082; -0.004 1.000 0.000 0.509; 0.065 0.000 0.998 -7.901; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 133 113 eigenvectors: -0.002 -0.003 1.000; -0.035 -0.999 -0.003; 0.999 -0.035 0.002; error in mid anterior detected - correcting... writing aseg with callosum to to /home/kutato/freesurfer/subjects/C1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.8 minutes #-------------------------------------- #@# Merge ASeg Wed Mar 3 22:14:45 CET 2010
cp aseg.auto.mgz aseg.mgz
#-------------------------------------------- #@# Intensity Normalization2 Wed Mar 3 22:14:45 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using control points from file /home/kutato/freesurfer/subjects/C1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 710 control points... only using 710 control points from file... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 223389 control points removed building Voronoi diagram... performing soap bubble smoothing... 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 brain.mgz 3D bias adjustment took 6 minutes and 6 seconds. using MR volume brainmask.mgz to mask input volume... using wm (255) threshold 245.0 for removing exterior voxels white matter peak found at 111 gm peak at 77 (77), valley at 40 (40) csf peak at 28, setting threshold to 60 white matter peak found at 111 gm peak at 78 (78), valley at 40 (40) csf peak at 29, setting threshold to 61 #-------------------------------------------- #@# Mask BFS Wed Mar 3 22:20:55 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Mar 3 22:20:58 CET 2010
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (109.0): 107.5 +- 7.5 [80.0 --> 125.0] GM (68.0) : 65.0 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10488 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4151 filled 110391 bright non-wm voxels segmented. 7168 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz...
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume... auto filling took 0.76 minutes reading wm segmentation from wm.seg.mgz... 404 voxels added to wm to prevent paths from MTL structures to cortex 6112 additional wm voxels added 0 additional wm voxels added SEG EDIT: 68648 voxels turned on, 46182 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 90 new 90 115,126,128 old 90 new 90 writing edited volume to wm.asegedit.mgz....
mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1 pass 1 (xy+): 154 found - 154 modified | TOTAL: 154 pass 2 (xy+): 0 found - 154 modified | TOTAL: 154 pass 1 (xy-): 134 found - 134 modified | TOTAL: 288 pass 2 (xy-): 0 found - 134 modified | TOTAL: 288 pass 1 (yz+): 124 found - 124 modified | TOTAL: 412 pass 2 (yz+): 0 found - 124 modified | TOTAL: 412 pass 1 (yz-): 99 found - 99 modified | TOTAL: 511 pass 2 (yz-): 0 found - 99 modified | TOTAL: 511 pass 1 (xz+): 137 found - 137 modified | TOTAL: 648 pass 2 (xz+): 0 found - 137 modified | TOTAL: 648 pass 1 (xz-): 124 found - 124 modified | TOTAL: 772 pass 2 (xz-): 0 found - 124 modified | TOTAL: 772 Iteration Number : 1 pass 1 (+++): 100 found - 100 modified | TOTAL: 100 pass 2 (+++): 0 found - 100 modified | TOTAL: 100 pass 1 (+++): 97 found - 97 modified | TOTAL: 197 pass 2 (+++): 0 found - 97 modified | TOTAL: 197 pass 1 (+++): 84 found - 84 modified | TOTAL: 281 pass 2 (+++): 0 found - 84 modified | TOTAL: 281 pass 1 (+++): 135 found - 135 modified | TOTAL: 416 pass 2 (+++): 0 found - 135 modified | TOTAL: 416 Iteration Number : 1 pass 1 (++): 141 found - 141 modified | TOTAL: 141 pass 2 (++): 0 found - 141 modified | TOTAL: 141 pass 1 (+-): 205 found - 205 modified | TOTAL: 346 pass 2 (+-): 0 found - 205 modified | TOTAL: 346 pass 1 (--): 152 found - 152 modified | TOTAL: 498 pass 2 (--): 1 found - 153 modified | TOTAL: 499 pass 3 (--): 0 found - 153 modified | TOTAL: 499 pass 1 (-+): 183 found - 183 modified | TOTAL: 682 pass 2 (-+): 0 found - 183 modified | TOTAL: 682 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 23 found - 23 modified | TOTAL: 45 pass 2 (xy-): 0 found - 23 modified | TOTAL: 45 pass 1 (yz+): 19 found - 19 modified | TOTAL: 64 pass 2 (yz+): 0 found - 19 modified | TOTAL: 64 pass 1 (yz-): 37 found - 37 modified | TOTAL: 101 pass 2 (yz-): 0 found - 37 modified | TOTAL: 101 pass 1 (xz+): 39 found - 39 modified | TOTAL: 140 pass 2 (xz+): 0 found - 39 modified | TOTAL: 140 pass 1 (xz-): 22 found - 22 modified | TOTAL: 162 pass 2 (xz-): 0 found - 22 modified | TOTAL: 162 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 pass 1 (+++): 4 found - 4 modified | TOTAL: 19 pass 2 (+++): 0 found - 4 modified | TOTAL: 19 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 22 found - 22 modified | TOTAL: 35 pass 2 (+-): 0 found - 22 modified | TOTAL: 35 pass 1 (--): 17 found - 17 modified | TOTAL: 52 pass 2 (--): 0 found - 17 modified | TOTAL: 52 pass 1 (-+): 10 found - 10 modified | TOTAL: 62 pass 2 (-+): 0 found - 10 modified | TOTAL: 62 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 2131 (out of 674704: 0.315842) keeping edits binarizing input wm segmentation... Ambiguous edge configurations...
Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels
mri_pretess done
#-------------------------------------------- #@# Fill Wed Mar 3 22:23:31 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 619 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 119, 151), TAL = (2.0, 23.0, 9.0) talairach voxel to voxel transform 0.943 0.014 0.050 -0.471; -0.002 0.809 -0.158 52.074; -0.063 0.140 0.999 12.198; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 119, 151) --> (2.0, 23.0, 9.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 23.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 9.00) SRC: (110.64, 124.32, 172.81) search lh wm seed point around talairach space (-16.00, 23.00, 9.00), SRC: (144.61, 124.24, 170.53) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Mar 3 22:24:28 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 12 found - 12 modified | TOTAL: 25 pass 2 (xy-): 0 found - 12 modified | TOTAL: 25 pass 1 (yz+): 10 found - 10 modified | TOTAL: 35 pass 2 (yz+): 0 found - 10 modified | TOTAL: 35 pass 1 (yz-): 22 found - 22 modified | TOTAL: 57 pass 2 (yz-): 0 found - 22 modified | TOTAL: 57 pass 1 (xz+): 15 found - 15 modified | TOTAL: 72 pass 2 (xz+): 0 found - 15 modified | TOTAL: 72 pass 1 (xz-): 5 found - 5 modified | TOTAL: 77 pass 2 (xz-): 0 found - 5 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 9 found - 9 modified | TOTAL: 15 pass 2 (+-): 0 found - 9 modified | TOTAL: 15 pass 1 (--): 13 found - 13 modified | TOTAL: 28 pass 2 (--): 0 found - 13 modified | TOTAL: 28 pass 1 (-+): 3 found - 3 modified | TOTAL: 31 pass 2 (-+): 0 found - 3 modified | TOTAL: 31 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 128 (out of 320366: 0.039954) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ slice 50: 715 vertices, 806 faces slice 60: 6587 vertices, 6870 faces slice 70: 16362 vertices, 16829 faces slice 80: 27996 vertices, 28461 faces slice 90: 40299 vertices, 40842 faces slice 100: 52688 vertices, 53229 faces slice 110: 65001 vertices, 65581 faces slice 120: 77662 vertices, 78249 faces slice 130: 89134 vertices, 89714 faces slice 140: 100712 vertices, 101362 faces slice 150: 112906 vertices, 113608 faces slice 160: 123188 vertices, 123863 faces slice 170: 130916 vertices, 131557 faces slice 180: 137022 vertices, 137584 faces slice 190: 141777 vertices, 142325 faces slice 200: 145789 vertices, 146310 faces slice 210: 149464 vertices, 149996 faces slice 220: 152836 vertices, 153278 faces slice 230: 152952 vertices, 153360 faces slice 240: 152952 vertices, 153360 faces slice 250: 152952 vertices, 153360 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components... 152952 voxel in cpt #1: X=-408 [v=152952,e=460080,f=306720] located at (-25.554226, -6.675813, -2.117488) For the whole surface: X=-408 [v=152952,e=460080,f=306720] One single component has been found nothing to do done
#-------------------------------------------- #@# Smooth1 lh Wed Mar 3 22:24:41 CET 2010
mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/kutato/freesurfer/subjects/C1/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Mar 3 22:24:46 CET 2010
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/kutato/freesurfer/subjects/C1/scripts avg radius = 49.0 mm, total surface area = 79501 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.071 (target=0.015) step 030: RMS=0.069 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.065 (target=0.015) step 045: RMS=0.065 (target=0.015) step 050: RMS=0.065 (target=0.015) step 055: RMS=0.065 (target=0.015) step 060: RMS=0.065 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Mar 3 22:25:42 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, sigma=0.0, host=local, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90
surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.88 (0.00-->27.18) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-1.82-->2.32) tol=1.0e-01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
301: dt: 15.53, sse: 8540.7 (0.052, 34.9, 0.000), neg: 26636 (%4.389:%4.53), avgs: 32 302: dt: 0.29, sse: 8539.7 (0.052, 34.9, 0.000), neg: 26636 (%4.375:%4.52), avgs: 32 303: dt: 0.29, sse: 8538.0 (0.052, 34.9, 0.000), neg: 26627 (%4.349:%4.52), avgs: 32 304: dt: 0.29, sse: 8536.1 (0.052, 34.9, 0.000), neg: 26615 (%4.318:%4.51), avgs: 32 305: dt: 0.29, sse: 8533.4 (0.052, 34.9, 0.000), neg: 26609 (%4.275:%4.50), avgs: 32 306: dt: 0.29, sse: 8530.6 (0.052, 34.8, 0.000), neg: 26596 (%4.228:%4.49), avgs: 32 307: dt: 0.29, sse: 8527.6 (0.052, 34.8, 0.000), neg: 26579 (%4.176:%4.48), avgs: 32 308: dt: 0.29, sse: 8524.4 (0.052, 34.8, 0.000), neg: 26560 (%4.119:%4.46), avgs: 32 309: dt: 0.29, sse: 8520.9 (0.052, 34.8, 0.000), neg: 26543 (%4.058:%4.45), avgs: 32 310: dt: 0.29, sse: 8517.4 (0.051, 34.8, 0.000), neg: 26523 (%3.994:%4.43), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->25.82) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.93-->2.40) 311: dt: 0.29, sse: 8514.0 (0.051, 34.8, 0.000), neg: 26509 (%3.932:%4.41), avgs: 32 312: dt: 48.14, sse: 8479.7 (0.051, 34.6, 0.000), neg: 26094 (%3.212:%4.03), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->24.45) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.71-->2.54) 313: dt: 3.56, sse: 8469.9 (0.051, 34.7, 0.000), neg: 26269 (%2.998:%4.03), avgs: 8 314: dt: 0.15, sse: 8469.3 (0.051, 34.7, 0.000), neg: 26242 (%2.986:%4.01), avgs: 8 315: dt: 0.15, sse: 8468.6 (0.051, 34.7, 0.000), neg: 26253 (%2.969:%4.00), avgs: 8 316: dt: 0.15, sse: 8467.1 (0.051, 34.7, 0.000), neg: 26267 (%2.942:%3.99), avgs: 8 317: dt: 0.15, sse: 8466.2 (0.051, 34.7, 0.000), neg: 26292 (%2.922:%3.98), avgs: 8 318: dt: 0.15, sse: 8465.3 (0.051, 34.7, 0.000), neg: 26295 (%2.901:%3.97), avgs: 8 319: dt: 0.15, sse: 8465.2 (0.051, 34.7, 0.000), neg: 26300 (%2.890:%3.96), avgs: 8 320: dt: 0.15, sse: 8464.7 (0.051, 34.7, 0.000), neg: 26310 (%2.872:%3.95), avgs: 8 vertex spacing 0.98 +- 0.88 (0.00-->23.63) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.52-->2.61) 321: dt: 0.15, sse: 8464.2 (0.051, 34.7, 0.000), neg: 26327 (%2.854:%3.94), avgs: 8 322: dt: 0.15, sse: 8463.7 (0.051, 34.7, 0.000), neg: 26343 (%2.835:%3.93), avgs: 8 323: dt: 0.15, sse: 8462.9 (0.051, 34.7, 0.000), neg: 26359 (%2.810:%3.93), avgs: 8 324: dt: 2.69, sse: 8458.0 (0.051, 34.7, 0.000), neg: 26415 (%2.703:%3.92), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->23.23) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.47-->2.64) 325: dt: 1.44, sse: 8454.2 (0.051, 34.7, 0.000), neg: 26661 (%2.601:%3.93), avgs: 2 326: dt: 0.09, sse: 8453.8 (0.051, 34.7, 0.000), neg: 26697 (%2.581:%3.93), avgs: 2 327: dt: 0.09, sse: 8452.8 (0.051, 34.8, 0.000), neg: 26737 (%2.553:%3.93), avgs: 2 328: dt: 0.09, sse: 8451.9 (0.051, 34.8, 0.000), neg: 26779 (%2.526:%3.92), avgs: 2 329: dt: 0.09, sse: 8451.5 (0.051, 34.8, 0.000), neg: 26818 (%2.503:%3.92), avgs: 2 330: dt: 0.09, sse: 8450.9 (0.051, 34.8, 0.000), neg: 26880 (%2.480:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.65) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.26-->2.69) 331: dt: 0.09, sse: 8450.2 (0.051, 34.8, 0.000), neg: 26944 (%2.455:%3.91), avgs: 2 332: dt: 0.09, sse: 8449.5 (0.051, 34.8, 0.000), neg: 27007 (%2.430:%3.92), avgs: 2 333: dt: 0.09, sse: 8449.1 (0.051, 34.8, 0.000), neg: 27074 (%2.410:%3.91), avgs: 2 334: dt: 0.09, sse: 8448.9 (0.051, 34.9, 0.000), neg: 27156 (%2.391:%3.92), avgs: 2 335: dt: 0.09, sse: 8448.2 (0.051, 34.9, 0.000), neg: 27231 (%2.368:%3.92), avgs: 2 336: dt: 0.06, sse: 8448.1 (0.051, 34.9, 0.000), neg: 27244 (%2.366:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.33) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.39-->2.72) 337: dt: 0.16, sse: 8447.2 (0.051, 34.9, 0.000), neg: 27436 (%2.337:%3.96), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.21-->2.72) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
338: dt: 107.53, sse: 1470.7 (0.051, 34.6, 0.000), neg: 26824 (%1.951:%3.54), avgs: 32 scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.782, avgs=0 005/300: dt: 0.9000, rms radial error=177.523, avgs=0 010/300: dt: 0.9000, rms radial error=176.967, avgs=0 015/300: dt: 0.9000, rms radial error=176.237, avgs=0 020/300: dt: 0.9000, rms radial error=175.406, avgs=0 025/300: dt: 0.9000, rms radial error=174.516, avgs=0 030/300: dt: 0.9000, rms radial error=173.592, avgs=0 035/300: dt: 0.9000, rms radial error=172.654, avgs=0 040/300: dt: 0.9000, rms radial error=171.710, avgs=0 045/300: dt: 0.9000, rms radial error=170.765, avgs=0 050/300: dt: 0.9000, rms radial error=169.821, avgs=0 055/300: dt: 0.9000, rms radial error=168.881, avgs=0 060/300: dt: 0.9000, rms radial error=167.944, avgs=0 065/300: dt: 0.9000, rms radial error=167.011, avgs=0 070/300: dt: 0.9000, rms radial error=166.083, avgs=0 075/300: dt: 0.9000, rms radial error=165.160, avgs=0 080/300: dt: 0.9000, rms radial error=164.243, avgs=0 085/300: dt: 0.9000, rms radial error=163.332, avgs=0 090/300: dt: 0.9000, rms radial error=162.426, avgs=0 095/300: dt: 0.9000, rms radial error=161.525, avgs=0 100/300: dt: 0.9000, rms radial error=160.628, avgs=0 105/300: dt: 0.9000, rms radial error=159.737, avgs=0 110/300: dt: 0.9000, rms radial error=158.850, avgs=0 115/300: dt: 0.9000, rms radial error=157.968, avgs=0 120/300: dt: 0.9000, rms radial error=157.091, avgs=0 125/300: dt: 0.9000, rms radial error=156.218, avgs=0 130/300: dt: 0.9000, rms radial error=155.350, avgs=0 135/300: dt: 0.9000, rms radial error=154.488, avgs=0 140/300: dt: 0.9000, rms radial error=153.631, avgs=0 145/300: dt: 0.9000, rms radial error=152.778, avgs=0 150/300: dt: 0.9000, rms radial error=151.929, avgs=0 155/300: dt: 0.9000, rms radial error=151.086, avgs=0 160/300: dt: 0.9000, rms radial error=150.246, avgs=0 165/300: dt: 0.9000, rms radial error=149.411, avgs=0 170/300: dt: 0.9000, rms radial error=148.581, avgs=0 175/300: dt: 0.9000, rms radial error=147.754, avgs=0 180/300: dt: 0.9000, rms radial error=146.933, avgs=0 185/300: dt: 0.9000, rms radial error=146.115, avgs=0 190/300: dt: 0.9000, rms radial error=145.302, avgs=0 195/300: dt: 0.9000, rms radial error=144.493, avgs=0 200/300: dt: 0.9000, rms radial error=143.688, avgs=0 205/300: dt: 0.9000, rms radial error=142.888, avgs=0 210/300: dt: 0.9000, rms radial error=142.091, avgs=0 215/300: dt: 0.9000, rms radial error=141.299, avgs=0 220/300: dt: 0.9000, rms radial error=140.511, avgs=0 225/300: dt: 0.9000, rms radial error=139.727, avgs=0 230/300: dt: 0.9000, rms radial error=138.948, avgs=0 235/300: dt: 0.9000, rms radial error=138.172, avgs=0 240/300: dt: 0.9000, rms radial error=137.401, avgs=0 245/300: dt: 0.9000, rms radial error=136.634, avgs=0 250/300: dt: 0.9000, rms radial error=135.871, avgs=0 255/300: dt: 0.9000, rms radial error=135.112, avgs=0 260/300: dt: 0.9000, rms radial error=134.358, avgs=0 265/300: dt: 0.9000, rms radial error=133.607, avgs=0 270/300: dt: 0.9000, rms radial error=132.860, avgs=0 275/300: dt: 0.9000, rms radial error=132.118, avgs=0 280/300: dt: 0.9000, rms radial error=131.379, avgs=0 285/300: dt: 0.9000, rms radial error=130.645, avgs=0 290/300: dt: 0.9000, rms radial error=129.914, avgs=0 295/300: dt: 0.9000, rms radial error=129.188, avgs=0 300/300: dt: 0.9000, rms radial error=128.465, avgs=0
spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 8624.98 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.02/37 = 0.00056 epoch 2 (K=80.0), pass 1, starting sse = 1491.66 integrating with navgs=32 and tol=3.200e+00 taking m339: dt: 0.29, sse: 1470.4 (0.051, 34.7, 0.000), neg: 26880 (%1.943:%3.54), avgs: 32 340: dt: 0.29, sse: 1470.0 (0.051, 34.7, 0.000), neg: 26948 (%1.935:%3.54), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.68) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.75) 341: dt: 0.29, sse: 1469.7 (0.051, 34.7, 0.000), neg: 27043 (%1.927:%3.55), avgs: 32 342: dt: 0.29, sse: 1469.3 (0.051, 34.7, 0.000), neg: 27089 (%1.919:%3.55), avgs: 32 343: dt: 0.29, sse: 1468.9 (0.051, 34.7, 0.000), neg: 27143 (%1.911:%3.55), avgs: 32 344: dt: 0.29, sse: 1468.5 (0.051, 34.7, 0.000), neg: 27154 (%1.903:%3.55), avgs: 32 345: dt: 0.29, sse: 1467.9 (0.051, 34.7, 0.000), neg: 27168 (%1.892:%3.54), avgs: 32 346: dt: 0.29, sse: 1467.6 (0.051, 34.7, 0.000), neg: 27200 (%1.886:%3.53), avgs: 32 347: dt: 0.29, sse: 1467.3 (0.051, 34.7, 0.000), neg: 27216 (%1.879:%3.53), avgs: 32 348: dt: 0.29, sse: 1466.8 (0.051, 34.7, 0.000), neg: 27228 (%1.870:%3.52), avgs: 32 349: dt: 36.97, sse: 1459.2 (0.051, 34.6, 0.000), neg: 27004 (%1.742:%3.40), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.80) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.79) 350: dt: 4.85, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27064 (%1.688:%3.39), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.81) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.21-->2.79) 351: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27067 (%1.685:%3.39), avgs: 8 352: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27083 (%1.684:%3.39), avgs: 8 353: dt: 0.15, sse: 1455.9 (0.051, 34.6, 0.000), neg: 27080 (%1.681:%3.37), avgs: 8 354: dt: 0.15, sse: 1456.3 (0.051, 34.6, 0.000), neg: 27102 (%1.684:%3.38), avgs: 8 355: dt: 0.15, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27124 (%1.681:%3.37), avgs: 8 356: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27155 (%1.679:%3.37), avgs: 8 357: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27182 (%1.677:%3.36), avgs: 8 358: dt: 0.15, sse: 1456.0 (0.051, 34.6, 0.000), neg: 27190 (%1.674:%3.36), avgs: 8 359: dt: 0.15, sse: 1455.8 (0.051, 34.6, 0.000), neg: 27194 (%1.669:%3.35), avgs: 8 360: dt: 0.15, sse: 1455.6 (0.051, 34.6, 0.000), neg: 27210 (%1.665:%3.35), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.92) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.80) 361: dt: 9.20, sse: 1452.7 (0.051, 34.6, 0.000), neg: 27182 (%1.611:%3.30), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.00) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.80) 362: dt: 0.77, sse: 1451.0 (0.051, 34.6, 0.000), neg: 27300 (%1.582:%3.32), avgs: 2 363: dt: 0.09, sse: 1450.6 (0.051, 34.6, 0.000), neg: 27301 (%1.575:%3.31), avgs: 2 364: dt: 0.09, sse: 1450.3 (0.051, 34.6, 0.000), neg: 27336 (%1.568:%3.31), avgs: 2 365: dt: 0.09, sse: 1449.7 (0.051, 34.6, 0.000), neg: 27352 (%1.556:%3.31), avgs: 2 366: dt: 0.09, sse: 1449.0 (0.051, 34.6, 0.000), neg: 27377 (%1.544:%3.32), avgs: 2 367: dt: 0.09, sse: 1448.6 (0.051, 34.6, 0.000), neg: 27398 (%1.536:%3.31), avgs: 2 368: dt: 0.09, sse: 1448.0 (0.051, 34.6, 0.000), neg: 27412 (%1.526:%3.31), avgs: 2 369: dt: 0.09, sse: 1447.4 (0.051, 34.6, 0.000), neg: 27438 (%1.514:%3.30), avgs: 2 370: dt: 0.09, sse: 1446.5 (0.051, 34.6, 0.000), neg: 27458 (%1.499:%3.30), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.08) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.14-->2.80) 371: dt: 0.09, sse: 1445.8 (0.051, 34.6, 0.000), neg: 27460 (%1.486:%3.29), avgs: 2 372: dt: 0.09, sse: 1445.1 (0.051, 34.6, 0.000), neg: 27497 (%1.474:%3.28), avgs: 2 373: dt: 1.48, sse: 1443.8 (0.051, 34.7, 0.000), neg: 27589 (%1.452:%3.29), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.12-->2.81) 374: dt: 0.27, sse: 1443.2 (0.051, 34.7, 0.000), neg: 27714 (%1.439:%3.27), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.29-->2.81) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
375: dt: 36.63, sse: 250.8 (0.051, 34.6, 0.000), neg: 27421 (%1.349:%3.19), avgs: 32 376: dt: 0.29, sse: 250.5 (0.051, 34.6, 0.000), neg: 27438 (%1.343:%3.19), avgs: 32 377: dt: 0.29, sse: 250.2 (0.051, 34.6, 0.000), neg: 27456 (%1.339:%3.18), avgs: 32 378: dt: 0.29, sse: 249.9 (0.051, 34.6, 0.000), neg: 27450 (%1.333:%3.17), avgs: 32 379: dt: 0.29, sse: 249.6 (0.051, 34.6, 0.000), neg: 27460 (%1.330:%3.16), avgs: 32 380: dt: 0.29, sse: 249.5 (0.051, 34.6, 0.000), neg: 27454 (%1.327:%3.15), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.32-->2.82) 381: dt: 0.29, sse: 249.4 (0.051, 34.6, 0.000), neg: 27446 (%1.325:%3.15), avgs: 32 382: dt: 0.29, sse: 249.2 (0.051, 34.6, 0.000), neg: 27444 (%1.322:%3.14), avgs: 32 383: dt: 0.29, sse: 249.0 (0.051, 34.6, 0.000), neg: 27438 (%1.319:%3.13), avgs: 32 384: dt: 0.29, sse: 248.9 (0.051, 34.6, 0.000), neg: 27421 (%1.317:%3.12), avgs: 32 385: dt: 0.29, sse: 248.7 (0.051, 34.6, 0.000), neg: 27418 (%1.313:%3.12), avgs: 32 386: dt: 155.64, sse: 241.3 (0.051, 34.3, 0.000), neg: 26865 (%1.190:%2.88), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.14) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.26-->2.81) 387: dt: 2.19, sse: 237.7 (0.051, 34.3, 0.000), neg: 26842 (%1.139:%2.86), avgs: 8 388: dt: 0.15, sse: 237.6 (0.051, 34.3, 0.000), neg: 26834 (%1.137:%2.87), avgs: 8 389: dt: 0.15, sse: 237.5 (0.051, 34.3, 0.000), neg: 26828 (%1.136:%2.87), avgs: 8 390: dt: 0.15, sse: 237.2 (0.051, 34.3, 0.000), neg: 26807 (%1.131:%2.86), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.18) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.27-->2.81) 391: dt: 0.15, sse: 236.9 (0.051, 34.3, 0.000), neg: 26807 (%1.126:%2.86), avgs: 8 392: dt: 0.15, sse: 236.5 (0.051, 34.3, 0.000), neg: 26810 (%1.121:%2.86), avgs: 8 393: dt: 0.15, sse: 236.2 (0.051, 34.3, 0.000), neg: 26798 (%1.116:%2.86), avgs: 8 394: dt: 0.15, sse: 235.8 (0.051, 34.3, 0.000), neg: 26789 (%1.110:%2.86), avgs: 8 395: dt: 0.15, sse: 235.5 (0.051, 34.3, 0.000), neg: 26775 (%1.105:%2.86), avgs: 8 396: dt: 0.15, sse: 235.2 (0.051, 34.3, 0.000), neg: 26753 (%1.100:%2.85), avgs: 8 397: dt: 0.15, sse: 234.8 (0.051, 34.3, 0.000), neg: 26743 (%1.094:%2.84), avgs: 8 398: dt: 15.35, sse: 232.1 (0.051, 34.2, 0.000), neg: 26547 (%1.053:%2.76), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.25-->2.82) 399: dt: 1.29, sse: 228.5 (0.051, 34.2, 0.000), neg: 26596 (%1.000:%2.76), avgs: 2 400: dt: 0.54, sse: 227.3 (0.051, 34.2, 0.000), neg: 26618 (%0.983:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.22-->2.82) 401: dt: 0.09, sse: 227.3 (0.051, 34.2, 0.000), neg: 26629 (%0.983:%2.75), avgs: 2 402: dt: 0.09, sse: 227.0 (0.051, 34.2, 0.000), neg: 26613 (%0.978:%2.75), avgs: 2 403: dt: 0.09, sse: 226.7 (0.051, 34.2, 0.000), neg: 26617 (%0.973:%2.76), avgs: 2 404: dt: 0.09, sse: 226.4 (0.051, 34.2, 0.000), neg: 26605 (%0.968:%2.76), avgs: 2 405: dt: 0.09, sse: 226.0 (0.051, 34.2, 0.000), neg: 26603 (%0.962:%2.76), avgs: 2 406: dt: 0.09, sse: 225.8 (0.051, 34.2, 0.000), neg: 26617 (%0.958:%2.77), avgs: 2 407: dt: 0.09, sse: 225.4 (0.051, 34.2, 0.000), neg: 26612 (%0.953:%2.77), avgs: 2 408: dt: 0.09, sse: 225.1 (0.051, 34.2, 0.000), neg: 26604 (%0.948:%2.77), avgs: 2 409: dt: 0.09, sse: 224.8 (0.051, 34.1, 0.000), neg: 26602 (%0.943:%2.76), avgs: 2 410: dt: 0.09, sse: 224.4 (0.051, 34.1, 0.000), neg: 26606 (%0.937:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.35) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 411: dt: 1.71, sse: 223.5 (0.051, 34.1, 0.000), neg: 26591 (%0.925:%2.71), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 412: dt: 0.03, sse: 223.1 (0.051, 34.1, 0.000), neg: 26666 (%0.918:%2.72), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
413: dt: 48.76, sse: 83.1 (0.051, 34.1, 0.000), neg: 26317 (%0.904:%2.68), avgs: 32 414: dt: 0.29, sse: 82.8 (0.051, 34.0, 0.000), neg: 26321 (%0.900:%2.68), avgs: 32 415: dt: 0.29, sse: 82.5 (0.051, 34.0, 0.000), neg: 26315 (%0.895:%2.68), avgs: 32 416: dt: 0.29, sse: 82.1 (0.051, 34.0, 0.000), neg: 26291 (%0.889:%2.67), avgs: 32 417: dt: 0.29, sse: 81.8 (0.051, 34.0, 0.000), neg: 26274 (%0.885:%2.67), avgs: 32 418: dt: 0.29, sse: 81.4 (0.051, 34.0, 0.000), neg: 26258 (%0.880:%2.66), avgs: 32 419: dt: 0.29, sse: 81.0 (0.051, 34.0, 0.000), neg: 26222 (%0.875:%2.65), avgs: 32 420: dt: 0.29, sse: 80.8 (0.051, 34.0, 0.000), neg: 26202 (%0.872:%2.64), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.29) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.84) 421: dt: 0.29, sse: 80.6 (0.051, 34.0, 0.000), neg: 26208 (%0.868:%2.64), avgs: 32 422: dt: 0.29, sse: 80.4 (0.051, 34.0, 0.000), neg: 26186 (%0.866:%2.64), avgs: 32 423: dt: 0.29, sse: 80.2 (0.051, 34.0, 0.000), neg: 26174 (%0.863:%2.64), avgs: 32 424: dt: 42.80, sse: 78.6 (0.051, 34.0, 0.000), neg: 26068 (%0.840:%2.60), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.84) 425: dt: 1.85, sse: 78.2 (0.051, 34.0, 0.000), neg: 26076 (%0.834:%2.57), avgs: 8 426: dt: 0.15, sse: 78.1 (0.051, 34.0, 0.000), neg: 26074 (%0.832:%2.57), avgs: 8 427: dt: 0.15, sse: 77.7 (0.051, 34.0, 0.000), neg: 26071 (%0.828:%2.57), avgs: 8 428: dt: 0.15, sse: 77.6 (0.051, 34.0, 0.000), neg: 26057 (%0.826:%2.57), avgs: 8 429: dt: 0.15, sse: 77.4 (0.051, 33.9, 0.000), neg: 26034 (%0.823:%2.57), avgs: 8 430: dt: 0.15, sse: 76.9 (0.051, 33.9, 0.000), neg: 26021 (%0.817:%2.56), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 431: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26008 (%0.814:%2.57), avgs: 8 432: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26015 (%0.814:%2.58), avgs: 8 433: dt: 0.15, sse: 76.5 (0.051, 33.9, 0.000), neg: 25996 (%0.811:%2.57), avgs: 8 434: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25991 (%0.808:%2.57), avgs: 8 435: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25997 (%0.808:%2.58), avgs: 8 436: dt: 1.20, sse: 76.2 (0.051, 33.9, 0.000), neg: 25992 (%0.805:%2.57), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 437: dt: 1.30, sse: 75.7 (0.051, 33.9, 0.000), neg: 26032 (%0.797:%2.57), avgs: 2 438: dt: 0.09, sse: 75.5 (0.051, 33.9, 0.000), neg: 26022 (%0.795:%2.57), avgs: 2 439: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26010 (%0.789:%2.56), avgs: 2 440: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26003 (%0.788:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.16) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.10-->2.85) 441: dt: 0.09, sse: 74.9 (0.051, 33.9, 0.000), neg: 26008 (%0.786:%2.57), avgs: 2 442: dt: 0.09, sse: 74.7 (0.051, 33.9, 0.000), neg: 26002 (%0.783:%2.57), avgs: 2 443: dt: 0.09, sse: 74.5 (0.051, 33.9, 0.000), neg: 26006 (%0.780:%2.58), avgs: 2 444: dt: 0.09, sse: 74.2 (0.051, 33.9, 0.000), neg: 26014 (%0.775:%2.58), avgs: 2 445: dt: 0.09, sse: 73.9 (0.051, 33.9, 0.000), neg: 26031 (%0.771:%2.58), avgs: 2 446: dt: 0.09, sse: 73.8 (0.051, 33.9, 0.000), neg: 26044 (%0.769:%2.59), avgs: 2 447: dt: 0.09, sse: 73.7 (0.051, 33.9, 0.000), neg: 26058 (%0.767:%2.61), avgs: 2 448: dt: 1.25, sse: 73.3 (0.051, 33.8, 0.000), neg: 25993 (%0.761:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.85) 449: dt: 0.03, sse: 73.2 (0.051, 33.8, 0.000), neg: 26076 (%0.760:%2.60), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.18-->2.85) 449: dt: 0.00, sse: 8423.5 (0.050, 33.8, 0.000), neg: 26076 (%0.754:%2.60), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours omentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.03/37 = 0.00088 epoch 3 (K=320.0), pass 1, starting sse = 256.64 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/38 = 0.00344 epoch 4 (K=1280.0), pass 1, starting sse = 83.95 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/37 = 0.00346 final distance error %100000.00 optimization complete. unfolding took 0.12 hours #-------------------------------------------- #@# Fix Topology lh Wed Mar 3 22:34:46 CET 2010
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/home/kutato/freesurfer/subjects/C1/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga C1 lh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters
************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0
************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ before topology correction, eno=-408 (nv=152952, nf=306720, ne=460080, g=205) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 56276 ambiguous faces found in tessellation segmenting defects... 92 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 4 -merging segment 0 into 5 -merging segment 29 into 27 -merging segment 32 into 30 -merging segment 71 into 49 -merging segment 4 into 52 -merging segment 74 into 72 85 defects to be corrected 0 vertices coincident reading input surface /home/kutato/freesurfer/subjects/C1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1015 (-4.5508) -vertex loglikelihood: -6.5092 (-3.2546) -normal dot loglikelihood: -3.5881 (-3.5881) -quad curv loglikelihood: -5.9652 (-2.9826) Total Loglikelihood : -25.1641
CORRECTING DEFECT 0 (vertices=48, convex hull=73) After retessellation of defect 0, euler #=-66 (121738,358994,237190) : difference with theory (-82) = -16
CORRECTING DEFECT 1 (vertices=172, convex hull=59) After retessellation of defect 1, euler #=-65 (121763,359092,237264) : difference with theory (-81) = -16
CORRECTING DEFECT 2 (vertices=14, convex hull=14) After retessellation of defect 2, euler #=-64 (121763,359095,237268) : difference with theory (-80) = -16
CORRECTING DEFECT 3 (vertices=4413, convex hull=721) After retessellation of defect 3, euler #=-67 (122638,362153,239448) : difference with theory (-79) = -12
CORRECTING DEFECT 4 (vertices=16, convex hull=21) After retessellation of defect 4, euler #=-66 (122639,362162,239457) : difference with theory (-78) = -12
CORRECTING DEFECT 5 (vertices=318, convex hull=123) After retessellation of defect 5, euler #=-65 (122682,362353,239606) : difference with theory (-77) = -12
CORRECTING DEFECT 6 (vertices=39, convex hull=81) After retessellation of defect 6, euler #=-64 (122698,362433,239671) : difference with theory (-76) = -12
CORRECTING DEFECT 7 (vertices=43, convex hull=30) After retessellation of defect 7, euler #=-63 (122702,362458,239693) : difference with theory (-75) = -12
CORRECTING DEFECT 8 (vertices=87, convex hull=103) After retessellation of defect 8, euler #=-62 (122736,362601,239803) : difference with theory (-74) = -12
CORRECTING DEFECT 9 (vertices=22, convex hull=52) After retessellation of defect 9, euler #=-61 (122744,362644,239839) : difference with theory (-73) = -12
CORRECTING DEFECT 10 (vertices=103, convex hull=78) After retessellation of defect 10, euler #=-60 (122768,362752,239924) : difference with theory (-72) = -12
CORRECTING DEFECT 11 (vertices=427, convex hull=253) After retessellation of defect 11, euler #=-59 (122927,363356,240370) : difference with theory (-71) = -12
CORRECTING DEFECT 12 (vertices=1508, convex hull=562) After retessellation of defect 12, euler #=-59 (123340,364897,241498) : difference with theory (-70) = -11
CORRECTING DEFECT 13 (vertices=57, convex hull=109) After retessellation of defect 13, euler #=-58 (123374,365043,241611) : difference with theory (-69) = -11
CORRECTING DEFECT 14 (vertices=49, convex hull=79) After retessellation of defect 14, euler #=-57 (123402,365159,241700) : difference with theory (-68) = -11
CORRECTING DEFECT 15 (vertices=69, convex hull=96) After retessellation of defect 15, euler #=-56 (123431,365288,241801) : difference with theory (-67) = -11
CORRECTING DEFECT 16 (vertices=29, convex hull=55) After retessellation of defect 16, euler #=-55 (123440,365339,241844) : difference with theory (-66) = -11
CORRECTING DEFECT 17 (vertices=14, convex hull=28) After retessellation of defect 17, euler #=-54 (123443,365354,241857) : difference with theory (-65) = -11
CORRECTING DEFECT 18 (vertices=41, convex hull=48) After retessellation of defect 18, euler #=-53 (123452,365398,241893) : difference with theory (-64) = -11
CORRECTING DEFECT 19 (vertices=459, convex hull=241) After retessellation of defect 19, euler #=-52 (123590,365935,242293) : difference with theory (-63) = -11
CORRECTING DEFECT 20 (vertices=55, convex hull=110) After retessellation of defect 20, euler #=-51 (123623,366080,242406) : difference with theory (-62) = -11
CORRECTING DEFECT 21 (vertices=478, convex hull=255) After retessellation of defect 21, euler #=-50 (123653,366319,242616) : difference with theory (-61) = -11
CORRECTING DEFECT 22 (vertices=27, convex hull=34) After retessellation of defect 22, euler #=-49 (123662,366357,242646) : difference with theory (-60) = -11
CORRECTING DEFECT 23 (vertices=53, convex hull=92) After retessellation of defect 23, euler #=-48 (123692,366487,242747) : difference with theory (-59) = -11
CORRECTING DEFECT 24 (vertices=32, convex hull=45) After retessellation of defect 24, euler #=-46 (123692,366504,242766) : difference with theory (-58) = -12
CORRECTING DEFECT 25 (vertices=181, convex hull=167) After retessellation of defect 25, euler #=-45 (123711,366644,242888) : difference with theory (-57) = -12
CORRECTING DEFECT 26 (vertices=1122, convex hull=340) After retessellation of defect 26, euler #=-45 (124058,367886,243783) : difference with theory (-56) = -11
CORRECTING DEFECT 27 (vertices=213, convex hull=67) After retessellation of defect 27, euler #=-44 (124080,367986,243862) : difference with theory (-55) = -11
CORRECTING DEFECT 28 (vertices=35, convex hull=22) After retessellation of defect 28, euler #=-43 (124085,368007,243879) : difference with theory (-54) = -11
CORRECTING DEFECT 29 (vertices=20, convex hull=63) After retessellation of defect 29, euler #=-42 (124095,368059,243922) : difference with theory (-53) = -11
CORRECTING DEFECT 30 (vertices=13, convex hull=26) After retessellation of defect 30, euler #=-41 (124096,368072,243935) : difference with theory (-52) = -11
CORRECTING DEFECT 31 (vertices=29, convex hull=74) After retessellation of defect 31, euler #=-40 (124105,368127,243982) : difference with theory (-51) = -11
CORRECTING DEFECT 32 (vertices=42, convex hull=33) After retessellation of defect 32, euler #=-39 (124109,368148,244000) : difference with theory (-50) = -11
CORRECTING DEFECT 33 (vertices=88, convex hull=93) After retessellation of defect 33, euler #=-38 (124124,368233,244071) : difference with theory (-49) = -11
CORRECTING DEFECT 34 (vertices=53, convex hull=67) After retessellation of defect 34, euler #=-37 (124137,368300,244126) : difference with theory (-48) = -11
CORRECTING DEFECT 35 (vertices=396, convex hull=152) After retessellation of defect 35, euler #=-36 (124283,368807,244488) : difference with theory (-47) = -11
CORRECTING DEFECT 36 (vertices=49, convex hull=71) After retessellation of defect 36, euler #=-35 (124310,368918,244573) : difference with theory (-46) = -11
CORRECTING DEFECT 37 (vertices=6, convex hull=20) After retessellation of defect 37, euler #=-34 (124311,368926,244581) : difference with theory (-45) = -11
CORRECTING DEFECT 38 (vertices=42, convex hull=81) After retessellation of defect 38, euler #=-33 (124337,369038,244668) : difference with theory (-44) = -11
CORRECTING DEFECT 39 (vertices=96, convex hull=66) After retessellation of defect 39, euler #=-32 (124378,369192,244782) : difference with theory (-43) = -11
CORRECTING DEFECT 40 (vertices=27, convex hull=34) After retessellation of defect 40, euler #=-31 (124382,369214,244801) : difference with theory (-42) = -11
CORRECTING DEFECT 41 (vertices=295, convex hull=174) After retessellation of defect 41, euler #=-30 (124455,369519,245034) : difference with theory (-41) = -11
CORRECTING DEFECT 42 (vertices=192, convex hull=126) After retessellation of defect 42, euler #=-29 (124483,369662,245150) : difference with theory (-40) = -11
CORRECTING DEFECT 43 (vertices=100, convex hull=110) After retessellation of defect 43, euler #=-28 (124549,369912,245335) : difference with theory (-39) = -11
CORRECTING DEFECT 44 (vertices=564, convex hull=398) After retessellation of defect 44, euler #=-27 (124766,370766,245973) : difference with theory (-38) = -11
CORRECTING DEFECT 45 (vertices=148, convex hull=121) After retessellation of defect 45, euler #=-26 (124843,371049,246180) : difference with theory (-37) = -11
CORRECTING DEFECT 46 (vertices=51, convex hull=75) After retessellation of defect 46, euler #=-25 (124855,371114,246234) : difference with theory (-36) = -11
CORRECTING DEFECT 47 (vertices=16122, convex hull=4397) normal vector of length zero at vertex 139578 with 0 faces vertex 139578 has 0 face Numerical result out of range Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 4 05:39:45 CET 2010
2010/3/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Gabor,
recon2-cp currently starts *after* the aseg, so you'll need to rerun it from an ealier point than that. Try using -autorecon2 instead.
cheers Bruce
On Wed, 3 Mar 2010, Perlaki Gabor wrote:
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
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hmmm, looks like there is a huge defect in the surface. Did you look at them to make sure nothing is very wrong (e.g. cerebellum attached to cortex)? Make sure you didn't include any control points in cerebellar gray matter, only in points that are in the interior of the white matter (and not for example in the dentate)
cheers, Bruce
On Thu, 4 Mar 2010, Gergely Orsi wrote:
Hi Bruce,
Thanks for your help. I've run the recon-all as you told (recon-all -autorecon2 -autorecon3 -subjid C1), but the recon-all exited with errors. I'm sending you the log. Could you help us some more?
Thank you.
Gergely Orsi
New invocation of recon-all
Wed Mar 3 16:00:17 CET 2010 /home/kutato/freesurfer/subjects/C1 /home/kutato/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid C1 subjid C1 setenv SUBJECTS_DIR /home/kutato/freesurfer/subjects FREESURFER_HOME /home/kutato/freesurfer Actual FREESURFER_HOME /home/kutato/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cachedMem: 4020216 2044228 1975988 0 182484 1237240 Swap: 8634360 0 8634360
######################################## program versions used $Id: recon-all,v 1.133.2.38 2009/01/08 19:49:55 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: tkregister2.c,v 1.86.2.7 2009/01/18 19:41:35 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_label.c,v 1.80.2.5 2008/08/15 21:00:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.5 2009/01/15 01:36:52 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature_stats.c,v 1.28.2.4 2008/10/02 21:42:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #------------------------------------- #@# EM Registration Wed Mar 3 16:00:18 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_em_register -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros)
spacing=8, using 2185 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 initial log_p = -84452.9
First Search limited to translation only.
Found translation: (-0.3, -12.2, -22.4): log p = -24312.3
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-24312.3 (thresh=-24288.0) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-12644.5 (thresh=-12631.8) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-12036.9, old_max_log_p =-12644.5 (thresh=-12631.8) 1.067 -0.009 -0.080 4.483; 0.020 1.198 0.188 -64.729; 0.090 -0.169 0.966 -5.663; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11905.9, old_max_log_p =-12036.9 (thresh=-12024.8) 1.050 -0.009 -0.079 6.394; 0.021 1.195 0.204 -66.521; 0.089 -0.185 0.948 -0.958; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11904.4, old_max_log_p =-11905.9 (thresh=-11894.0) 1.050 0.011 -0.076 3.377; 0.004 1.214 0.208 -67.391; 0.090 -0.188 0.963 -2.618; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11904.4 (thresh=-11892.5) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11516.2 (thresh=-11504.7) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 2185 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 11516.2 tol 0.000010 Resulting transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -11516.2 (old=-84452.9) transform before final EM align: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 244171 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1559944.8 tol 0.000000 final transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta... registration took 38 minutes and 54 seconds. #-------------------------------------- #@# CA Normalize Wed Mar 3 16:39:12 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
reading manually defined control points from /home/kutato/freesurfer/subjects/C1/tmp/control.dat using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 using 244171 sample points... INFO: compute sample coordinates transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 109.0 164 of 520 (31.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 112.0 208 of 519 (40.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 117.0 3 of 14 (21.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 121.0 4 of 21 (19.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 101.0 --> 116.0 6 of 51 (11.8%) samples deleted using 1125 total control points for intensity normalization... bias field = 1.011 +- 0.076 0 of 1450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 171 of 491 (34.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 113.0 132 of 559 (23.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 116.0 16 of 67 (23.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 117.0 10 of 70 (14.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 99.0 --> 113.0 12 of 94 (12.8%) samples deleted using 1281 total control points for intensity normalization... bias field = 0.994 +- 0.088 0 of 1650 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 210 of 555 (37.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 168 of 597 (28.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 113.0 21 of 79 (26.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 113.0 19 of 85 (22.4%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 91.0 --> 106.0 64 of 179 (35.8%) samples deleted using 1495 total control points for intensity normalization... bias field = 0.997 +- 0.082 0 of 1723 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Wed Mar 3 16:40:49 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.27 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.766, neg=0, invalid=766 0001: dt=228.525253, rms=0.731 (4.651%), neg=0, invalid=766 0002: dt=230.826667, rms=0.716 (1.976%), neg=0, invalid=766 0003: dt=131.235955, rms=0.711 (0.775%), neg=0, invalid=766 0004: dt=369.920000, rms=0.705 (0.719%), neg=0, invalid=766 0005: dt=134.901961, rms=0.702 (0.467%), neg=0, invalid=766 0006: dt=295.936000, rms=0.700 (0.338%), neg=0, invalid=766 0007: dt=129.472000, rms=0.698 (0.295%), neg=0, invalid=766 0008: dt=443.904000, rms=0.696 (0.269%), neg=0, invalid=766 0009: dt=142.933333, rms=0.694 (0.331%), neg=0, invalid=766 0010: dt=129.472000, rms=0.693 (0.073%), neg=0, invalid=766 0011: dt=129.472000, rms=0.692 (0.120%), neg=0, invalid=766 0012: dt=129.472000, rms=0.691 (0.183%), neg=0, invalid=766 0013: dt=129.472000, rms=0.689 (0.236%), neg=0, invalid=766 0014: dt=129.472000, rms=0.688 (0.265%), neg=0, invalid=766 0015: dt=129.472000, rms=0.686 (0.290%), neg=0, invalid=766 0016: dt=129.472000, rms=0.684 (0.282%), neg=0, invalid=766 0017: dt=129.472000, rms=0.682 (0.255%), neg=0, invalid=766 0018: dt=129.472000, rms=0.680 (0.239%), neg=0, invalid=766 0019: dt=129.472000, rms=0.679 (0.216%), neg=0, invalid=766 0020: dt=129.472000, rms=0.677 (0.204%), neg=0, invalid=766 0021: dt=129.472000, rms=0.676 (0.193%), neg=0, invalid=766 0022: dt=129.472000, rms=0.675 (0.166%), neg=0, invalid=766 0023: dt=129.472000, rms=0.674 (0.165%), neg=0, invalid=766 0024: dt=129.472000, rms=0.673 (0.171%), neg=0, invalid=766 0025: dt=129.472000, rms=0.672 (0.159%), neg=0, invalid=766 0026: dt=129.472000, rms=0.671 (0.137%), neg=0, invalid=766 0027: dt=129.472000, rms=0.670 (0.106%), neg=0, invalid=766 0028: dt=129.472000, rms=0.669 (0.111%), neg=0, invalid=766 0029: dt=129.472000, rms=0.668 (0.128%), neg=0, invalid=766 0030: dt=129.472000, rms=0.668 (0.109%), neg=0, invalid=766 0031: dt=129.472000, rms=0.667 (0.086%), neg=0, invalid=766 0032: dt=517.888000, rms=0.667 (0.023%), neg=0, invalid=766 0033: dt=517.888000, rms=0.667 (0.014%), neg=0, invalid=766 0034: dt=517.888000, rms=0.667 (-1.199%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0035: dt=129.472000, rms=0.665 (0.222%), neg=0, invalid=766 0036: dt=517.888000, rms=0.664 (0.233%), neg=0, invalid=766 0037: dt=129.472000, rms=0.664 (0.033%), neg=0, invalid=766 0038: dt=129.472000, rms=0.663 (0.026%), neg=0, invalid=766 0039: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0040: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0041: dt=129.472000, rms=0.662 (0.070%), neg=0, invalid=766 0042: dt=129.472000, rms=0.662 (0.085%), neg=0, invalid=766 0043: dt=129.472000, rms=0.661 (0.081%), neg=0, invalid=766 0044: dt=129.472000, rms=0.661 (0.066%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0045: dt=134.243902, rms=0.662 (0.847%), neg=0, invalid=766 0046: dt=136.900662, rms=0.651 (1.582%), neg=0, invalid=766 0047: dt=38.171429, rms=0.648 (0.467%), neg=0, invalid=766 0048: dt=145.152000, rms=0.645 (0.545%), neg=0, invalid=766 0049: dt=115.559395, rms=0.639 (0.880%), neg=0, invalid=766 0050: dt=36.288000, rms=0.638 (0.223%), neg=0, invalid=766 0051: dt=36.288000, rms=0.637 (0.131%), neg=0, invalid=766 0052: dt=36.288000, rms=0.635 (0.241%), neg=0, invalid=766 0053: dt=36.288000, rms=0.633 (0.377%), neg=0, invalid=766 0054: dt=36.288000, rms=0.630 (0.495%), neg=0, invalid=766 0055: dt=36.288000, rms=0.626 (0.531%), neg=0, invalid=766 0056: dt=36.288000, rms=0.623 (0.511%), neg=0, invalid=766 0057: dt=36.288000, rms=0.620 (0.485%), neg=0, invalid=766 0058: dt=36.288000, rms=0.617 (0.438%), neg=0, invalid=766 0059: dt=36.288000, rms=0.615 (0.421%), neg=0, invalid=766 0060: dt=36.288000, rms=0.612 (0.398%), neg=0, invalid=766 0061: dt=36.288000, rms=0.610 (0.353%), neg=0, invalid=766 0062: dt=36.288000, rms=0.609 (0.288%), neg=0, invalid=766 0063: dt=36.288000, rms=0.607 (0.241%), neg=0, invalid=766 0064: dt=36.288000, rms=0.606 (0.222%), neg=0, invalid=766 0065: dt=36.288000, rms=0.604 (0.208%), neg=0, invalid=766 0066: dt=36.288000, rms=0.603 (0.189%), neg=0, invalid=766 0067: dt=36.288000, rms=0.602 (0.167%), neg=0, invalid=766 0068: dt=36.288000, rms=0.601 (0.138%), neg=0, invalid=766 0069: dt=36.288000, rms=0.601 (0.134%), neg=0, invalid=766 0070: dt=36.288000, rms=0.600 (0.136%), neg=0, invalid=766 0071: dt=36.288000, rms=0.599 (0.142%), neg=0, invalid=766 0072: dt=36.288000, rms=0.598 (0.122%), neg=0, invalid=766 0073: dt=36.288000, rms=0.598 (0.110%), neg=0, invalid=766 0074: dt=124.416000, rms=0.597 (0.030%), neg=0, invalid=766 0075: dt=124.416000, rms=0.597 (-0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0076: dt=97.215190, rms=0.596 (0.268%), neg=0, invalid=766 0077: dt=37.647059, rms=0.595 (0.061%), neg=0, invalid=766 0078: dt=37.647059, rms=0.595 (0.033%), neg=0, invalid=766 0079: dt=37.647059, rms=0.595 (0.049%), neg=0, invalid=766 0080: dt=37.647059, rms=0.595 (0.050%), neg=0, invalid=766 0081: dt=37.647059, rms=0.594 (0.046%), neg=0, invalid=766 0082: dt=37.647059, rms=0.594 (0.028%), neg=0, invalid=766 0083: dt=36.288000, rms=0.594 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.59 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0084: dt=4.000000, rms=0.621 (0.022%), neg=0, invalid=766 0085: dt=1.600000, rms=0.621 (0.002%), neg=0, invalid=766 0086: dt=1.600000, rms=0.621 (0.001%), neg=0, invalid=766 0087: dt=1.600000, rms=0.621 (-0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0088: dt=1.600000, rms=0.621 (0.003%), neg=0, invalid=766 0089: dt=0.175000, rms=0.621 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0090: dt=5.778409, rms=0.671 (3.273%), neg=0, invalid=766 0091: dt=4.807692, rms=0.668 (0.356%), neg=0, invalid=766 0092: dt=2.304000, rms=0.668 (0.026%), neg=0, invalid=766 0093: dt=2.304000, rms=0.668 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 0094: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 0095: dt=0.384000, rms=0.717 (0.063%), neg=0, invalid=766 0096: dt=0.514706, rms=0.717 (0.077%), neg=0, invalid=766 0097: dt=1.280000, rms=0.716 (0.178%), neg=0, invalid=766 0098: dt=2.622951, rms=0.712 (0.483%), neg=0, invalid=766 0099: dt=0.448000, rms=0.712 (0.022%), neg=0, invalid=766 0100: dt=0.448000, rms=0.712 (0.029%), neg=0, invalid=766 0101: dt=0.448000, rms=0.711 (0.051%), neg=0, invalid=766 0102: dt=0.448000, rms=0.711 (0.065%), neg=0, invalid=766 0103: dt=0.448000, rms=0.711 (0.069%), neg=0, invalid=766 0104: dt=0.448000, rms=0.710 (0.049%), neg=0, invalid=766 0105: dt=0.448000, rms=0.710 (0.002%), neg=0, invalid=766 0106: dt=1.280000, rms=0.710 (0.013%), neg=0, invalid=766 0107: dt=3.307692, rms=0.709 (0.091%), neg=0, invalid=766 0108: dt=0.384000, rms=0.709 (0.016%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=766 0109: dt=1.024000, rms=0.709 (0.098%), neg=0, invalid=766 0110: dt=0.000000, rms=0.709 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=766 0111: dt=0.768240, rms=0.672 (2.434%), neg=0, invalid=766 0112: dt=0.028000, rms=0.671 (0.144%), neg=0, invalid=766 0113: dt=0.028000, rms=0.671 (-0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.671, neg=0, invalid=766 0114: dt=0.016000, rms=0.670 (0.020%), neg=0, invalid=766 0115: dt=0.000000, rms=0.670 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13848 (32) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, peak = 31), gca=30.6 gca peak = 0.14022 (22) mri peak = 0.14987 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, overlap=0.258) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, peak = 31), gca=31.3 gca peak = 0.24234 (100) mri peak = 0.17616 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.15860 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, overlap=0.633) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.09927 (79) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, peak = 77), gca=77.2 gca peak = 0.29892 (64) mri peak = 0.08177 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, overlap=0.005) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.06542 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.05686 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.02314 (77) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, peak = 80), gca=80.3 gca peak = 0.13270 (63) mri peak = 0.02476 (84) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, peak = 77), gca=77.2 gca peak = 0.15182 (70) mri peak = 0.16579 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, peak = 82), gca=82.2 gca peak = 0.14251 (76) mri peak = 0.22639 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, overlap=0.339) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.02272 (74) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, peak = 80), gca=79.5 gca peak = 0.12723 (61) mri peak = 0.02272 (77) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, peak = 82), gca=82.3 gca peak = 0.22684 (88) mri peak = 0.06491 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, peak = 112), gca=112.2 gca peak = 0.21067 (87) mri peak = 0.06839 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, peak = 109), gca=108.8 gca peak = 0.25455 (62) mri peak = 0.16005 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, peak = 78), gca=77.5 gca peak = 0.39668 (62) mri peak = 0.19364 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.08041 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, overlap=0.801) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.08539 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, overlap=0.548) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, peak = 98), gca=97.9 gca peak = 0.13716 (82) mri peak = 0.09766 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, overlap=0.375) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, peak = 92), gca=92.2 gca peak = 0.15214 (84) mri peak = 0.10719 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, overlap=0.371) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.08349 (101) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, overlap=0.001) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, peak = 102), gca=102.0 gca peak = 0.11809 (92) mri peak = 0.09947 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07866 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.19514 (33) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, overlap=0.860) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, peak = 32), gca=32.4 gca peak = 0.13542 (27) mri peak = 0.12763 (32) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, peak = 34), gca=34.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.22 x + 0.0 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... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0116: dt=108.542373, rms=0.671 (3.115%), neg=0, invalid=766 0117: dt=247.972125, rms=0.664 (1.098%), neg=0, invalid=766 0118: dt=192.927536, rms=0.659 (0.715%), neg=0, invalid=766 0119: dt=87.482014, rms=0.657 (0.292%), neg=0, invalid=766 0120: dt=517.888000, rms=0.653 (0.661%), neg=0, invalid=766 0121: dt=77.748148, rms=0.651 (0.220%), neg=0, invalid=766 0122: dt=2071.552000, rms=0.643 (1.306%), neg=0, invalid=766 0123: dt=71.896869, rms=0.640 (0.383%), neg=0, invalid=766 0124: dt=129.472000, rms=0.640 (0.109%), neg=0, invalid=766 0125: dt=517.888000, rms=0.637 (0.376%), neg=0, invalid=766 0126: dt=73.984000, rms=0.637 (0.062%), neg=0, invalid=766 0127: dt=887.808000, rms=0.635 (0.288%), neg=0, invalid=766 0128: dt=129.472000, rms=0.634 (0.235%), neg=0, invalid=766 0129: dt=517.888000, rms=0.633 (0.150%), neg=0, invalid=766 0130: dt=129.472000, rms=0.632 (0.119%), neg=0, invalid=766 0131: dt=295.936000, rms=0.631 (0.082%), neg=0, invalid=766 0132: dt=129.472000, rms=0.631 (0.085%), neg=0, invalid=766 0133: dt=221.952000, rms=0.630 (0.065%), neg=0, invalid=766 0134: dt=129.472000, rms=0.630 (0.073%), neg=0, invalid=766 0135: dt=295.936000, rms=0.630 (0.058%), neg=0, invalid=766 0136: dt=129.472000, rms=0.629 (0.094%), neg=0, invalid=766 0137: dt=110.976000, rms=0.629 (0.022%), neg=0, invalid=766 0138: dt=110.976000, rms=0.629 (0.053%), neg=0, invalid=766 0139: dt=110.976000, rms=0.628 (0.073%), neg=0, invalid=766 0140: dt=110.976000, rms=0.628 (0.081%), neg=0, invalid=766 0141: dt=110.976000, rms=0.627 (0.103%), neg=0, invalid=766 0142: dt=110.976000, rms=0.626 (0.149%), neg=0, invalid=766 0143: dt=110.976000, rms=0.625 (0.151%), neg=0, invalid=766 0144: dt=110.976000, rms=0.624 (0.152%), neg=0, invalid=766 0145: dt=110.976000, rms=0.623 (0.156%), neg=0, invalid=766 0146: dt=110.976000, rms=0.622 (0.160%), neg=0, invalid=766 0147: dt=110.976000, rms=0.621 (0.164%), neg=0, invalid=766 0148: dt=110.976000, rms=0.620 (0.157%), neg=0, invalid=766 0149: dt=110.976000, rms=0.619 (0.155%), neg=0, invalid=766 0150: dt=110.976000, rms=0.618 (0.154%), neg=0, invalid=766 0151: dt=110.976000, rms=0.617 (0.144%), neg=0, invalid=766 0152: dt=110.976000, rms=0.617 (0.122%), neg=0, invalid=766 0153: dt=110.976000, rms=0.616 (0.134%), neg=0, invalid=766 0154: dt=110.976000, rms=0.615 (0.147%), neg=0, invalid=766 0155: dt=110.976000, rms=0.614 (0.136%), neg=0, invalid=766 0156: dt=110.976000, rms=0.613 (0.119%), neg=0, invalid=766 0157: dt=110.976000, rms=0.613 (0.094%), neg=0, invalid=766 0158: dt=110.976000, rms=0.612 (0.112%), neg=0, invalid=766 0159: dt=110.976000, rms=0.611 (0.119%), neg=0, invalid=766 0160: dt=110.976000, rms=0.611 (0.098%), neg=0, invalid=766 0161: dt=110.976000, rms=0.610 (0.070%), neg=0, invalid=766 0162: dt=110.976000, rms=0.610 (0.093%), neg=0, invalid=766 0163: dt=110.976000, rms=0.609 (0.101%), neg=0, invalid=766 0164: dt=110.976000, rms=0.609 (0.086%), neg=0, invalid=766 0165: dt=110.976000, rms=0.608 (0.069%), neg=0, invalid=766 0166: dt=110.976000, rms=0.608 (0.081%), neg=0, invalid=766 0167: dt=110.976000, rms=0.607 (0.080%), neg=0, invalid=766 0168: dt=110.976000, rms=0.607 (0.067%), neg=0, invalid=766 0169: dt=110.976000, rms=0.606 (0.054%), neg=0, invalid=766 0170: dt=110.976000, rms=0.606 (0.060%), neg=0, invalid=766 0171: dt=110.976000, rms=0.606 (0.064%), neg=0, invalid=766 0172: dt=110.976000, rms=0.605 (0.066%), neg=0, invalid=766 0173: dt=110.976000, rms=0.605 (0.054%), neg=0, invalid=766 0174: dt=110.976000, rms=0.605 (0.053%), neg=0, invalid=766 0175: dt=110.976000, rms=0.604 (0.052%), neg=0, invalid=766 0176: dt=110.976000, rms=0.604 (0.048%), neg=0, invalid=766 0177: dt=110.976000, rms=0.604 (0.045%), neg=0, invalid=766 0178: dt=110.976000, rms=0.604 (0.043%), neg=0, invalid=766 0179: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=766 0180: dt=110.976000, rms=0.603 (0.050%), neg=0, invalid=766 0181: dt=110.976000, rms=0.603 (0.047%), neg=0, invalid=766 0182: dt=110.976000, rms=0.602 (0.035%), neg=0, invalid=766 0183: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=766 0184: dt=110.976000, rms=0.602 (0.040%), neg=0, invalid=766 0185: dt=110.976000, rms=0.602 (0.037%), neg=0, invalid=766 0186: dt=110.976000, rms=0.602 (0.033%), neg=0, invalid=766 0187: dt=110.976000, rms=0.601 (0.037%), neg=0, invalid=766 0188: dt=110.976000, rms=0.601 (0.030%), neg=0, invalid=766 0189: dt=110.976000, rms=0.601 (0.035%), neg=0, invalid=766 0190: dt=110.976000, rms=0.601 (0.040%), neg=0, invalid=766 0191: dt=110.976000, rms=0.601 (0.031%), neg=0, invalid=766 0192: dt=110.976000, rms=0.600 (0.027%), neg=0, invalid=766 0193: dt=110.976000, rms=0.600 (0.038%), neg=0, invalid=766 0194: dt=110.976000, rms=0.600 (0.035%), neg=0, invalid=766 0195: dt=110.976000, rms=0.600 (0.023%), neg=0, invalid=766 0196: dt=110.976000, rms=0.600 (0.028%), neg=0, invalid=766 0197: dt=110.976000, rms=0.599 (0.032%), neg=0, invalid=766 0198: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0199: dt=110.976000, rms=0.599 (0.027%), neg=0, invalid=766 0200: dt=110.976000, rms=0.599 (0.026%), neg=0, invalid=766 0201: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0202: dt=110.976000, rms=0.599 (0.028%), neg=0, invalid=766 0203: dt=110.976000, rms=0.598 (0.022%), neg=0, invalid=766 0204: dt=110.976000, rms=0.598 (0.032%), neg=0, invalid=766 0205: dt=110.976000, rms=0.598 (0.028%), neg=0, invalid=766 0206: dt=110.976000, rms=0.598 (0.021%), neg=0, invalid=766 0207: dt=110.976000, rms=0.598 (0.023%), neg=0, invalid=766 0208: dt=110.976000, rms=0.598 (0.024%), neg=0, invalid=766 0209: dt=110.976000, rms=0.598 (0.025%), neg=0, invalid=766 0210: dt=110.976000, rms=0.597 (0.020%), neg=0, invalid=766 0211: dt=221.952000, rms=0.597 (0.001%), neg=0, invalid=766 0212: dt=221.952000, rms=0.597 (0.014%), neg=0, invalid=766 0213: dt=221.952000, rms=0.597 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0214: dt=221.952000, rms=0.597 (0.077%), neg=0, invalid=766 0215: dt=443.904000, rms=0.596 (0.152%), neg=0, invalid=766 0216: dt=32.368000, rms=0.596 (0.018%), neg=0, invalid=766 0217: dt=32.368000, rms=0.596 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 0218: dt=112.375587, rms=0.596 (0.426%), neg=0, invalid=766 0219: dt=67.729134, rms=0.592 (0.773%), neg=0, invalid=766 0220: dt=31.104000, rms=0.590 (0.211%), neg=0, invalid=766 0221: dt=580.608000, rms=0.577 (2.307%), neg=0, invalid=766 0222: dt=64.000000, rms=0.574 (0.535%), neg=0, invalid=766 0223: dt=25.920000, rms=0.573 (0.091%), neg=0, invalid=766 0224: dt=331.776000, rms=0.571 (0.410%), neg=0, invalid=766 0225: dt=50.070588, rms=0.568 (0.559%), neg=0, invalid=766 0226: dt=20.736000, rms=0.567 (0.042%), neg=0, invalid=766 0227: dt=20.736000, rms=0.567 (0.035%), neg=0, invalid=766 0228: dt=20.736000, rms=0.567 (0.064%), neg=0, invalid=766 0229: dt=20.736000, rms=0.566 (0.111%), neg=0, invalid=766 0230: dt=20.736000, rms=0.565 (0.159%), neg=0, invalid=766 0231: dt=20.736000, rms=0.564 (0.176%), neg=0, invalid=766 0232: dt=20.736000, rms=0.563 (0.180%), neg=0, invalid=766 0233: dt=20.736000, rms=0.562 (0.180%), neg=0, invalid=766 0234: dt=20.736000, rms=0.561 (0.186%), neg=0, invalid=766 0235: dt=20.736000, rms=0.560 (0.201%), neg=0, invalid=766 0236: dt=20.736000, rms=0.559 (0.226%), neg=0, invalid=766 0237: dt=20.736000, rms=0.558 (0.230%), neg=0, invalid=766 0238: dt=20.736000, rms=0.556 (0.228%), neg=0, invalid=766 0239: dt=20.736000, rms=0.555 (0.216%), neg=0, invalid=766 0240: dt=20.736000, rms=0.554 (0.199%), neg=0, invalid=766 0241: dt=20.736000, rms=0.553 (0.192%), neg=0, invalid=766 0242: dt=20.736000, rms=0.552 (0.199%), neg=0, invalid=766 0243: dt=20.736000, rms=0.551 (0.198%), neg=0, invalid=766 0244: dt=20.736000, rms=0.550 (0.186%), neg=0, invalid=766 0245: dt=20.736000, rms=0.549 (0.175%), neg=0, invalid=766 0246: dt=20.736000, rms=0.548 (0.168%), neg=0, invalid=766 0247: dt=20.736000, rms=0.547 (0.160%), neg=0, invalid=766 0248: dt=20.736000, rms=0.546 (0.158%), neg=0, invalid=766 0249: dt=20.736000, rms=0.545 (0.159%), neg=0, invalid=766 0250: dt=20.736000, rms=0.544 (0.150%), neg=0, invalid=766 0251: dt=20.736000, rms=0.544 (0.138%), neg=0, invalid=766 0252: dt=20.736000, rms=0.543 (0.131%), neg=0, invalid=766 0253: dt=20.736000, rms=0.542 (0.127%), neg=0, invalid=766 0254: dt=20.736000, rms=0.542 (0.119%), neg=0, invalid=766 0255: dt=20.736000, rms=0.541 (0.117%), neg=0, invalid=766 0256: dt=20.736000, rms=0.540 (0.117%), neg=0, invalid=766 0257: dt=20.736000, rms=0.540 (0.109%), neg=0, invalid=766 0258: dt=20.736000, rms=0.539 (0.104%), neg=0, invalid=766 0259: dt=20.736000, rms=0.539 (0.098%), neg=0, invalid=766 0260: dt=20.736000, rms=0.538 (0.095%), neg=0, invalid=766 0261: dt=20.736000, rms=0.538 (0.093%), neg=0, invalid=766 0262: dt=20.736000, rms=0.537 (0.087%), neg=0, invalid=766 0263: dt=20.736000, rms=0.537 (0.081%), neg=0, invalid=766 0264: dt=20.736000, rms=0.536 (0.076%), neg=0, invalid=766 0265: dt=20.736000, rms=0.536 (0.075%), neg=0, invalid=766 0266: dt=20.736000, rms=0.535 (0.074%), neg=0, invalid=766 0267: dt=20.736000, rms=0.535 (0.073%), neg=0, invalid=766 0268: dt=20.736000, rms=0.535 (0.071%), neg=0, invalid=766 0269: dt=20.736000, rms=0.534 (0.067%), neg=0, invalid=766 0270: dt=20.736000, rms=0.534 (0.068%), neg=0, invalid=766 0271: dt=20.736000, rms=0.534 (0.066%), neg=0, invalid=766 0272: dt=20.736000, rms=0.533 (0.063%), neg=0, invalid=766 0273: dt=20.736000, rms=0.533 (0.058%), neg=0, invalid=766 0274: dt=20.736000, rms=0.533 (0.062%), neg=0, invalid=766 0275: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0276: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0277: dt=20.736000, rms=0.532 (0.059%), neg=0, invalid=766 0278: dt=20.736000, rms=0.531 (0.054%), neg=0, invalid=766 0279: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0280: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0281: dt=20.736000, rms=0.531 (0.045%), neg=0, invalid=766 0282: dt=20.736000, rms=0.530 (0.047%), neg=0, invalid=766 0283: dt=20.736000, rms=0.530 (0.050%), neg=0, invalid=766 0284: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0285: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0286: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0287: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0288: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0289: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0290: dt=20.736000, rms=0.529 (0.037%), neg=0, invalid=766 0291: dt=20.736000, rms=0.528 (0.037%), neg=0, invalid=766 0292: dt=20.736000, rms=0.528 (0.033%), neg=0, invalid=766 0293: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0294: dt=20.736000, rms=0.528 (0.035%), neg=0, invalid=766 0295: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0296: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0297: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0298: dt=20.736000, rms=0.527 (0.030%), neg=0, invalid=766 0299: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0300: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0301: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0302: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0303: dt=20.736000, rms=0.526 (0.031%), neg=0, invalid=766 0304: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0305: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0306: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0307: dt=20.736000, rms=0.526 (0.024%), neg=0, invalid=766 0308: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0309: dt=20.736000, rms=0.526 (0.027%), neg=0, invalid=766 0310: dt=20.736000, rms=0.526 (0.023%), neg=0, invalid=766 0311: dt=20.736000, rms=0.525 (0.026%), neg=0, invalid=766 0312: dt=20.736000, rms=0.525 (0.022%), neg=0, invalid=766 0313: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0314: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0315: dt=580.608000, rms=0.525 (0.040%), neg=0, invalid=766 0316: dt=31.104000, rms=0.525 (0.015%), neg=0, invalid=766 0317: dt=31.104000, rms=0.525 (0.007%), neg=0, invalid=766 0318: dt=31.104000, rms=0.525 (0.004%), neg=0, invalid=766 0319: dt=31.104000, rms=0.525 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=766 0320: dt=136.072072, rms=0.523 (0.371%), neg=0, invalid=766 0321: dt=36.288000, rms=0.522 (0.046%), neg=0, invalid=766 0322: dt=36.288000, rms=0.522 (0.054%), neg=0, invalid=766 0323: dt=36.288000, rms=0.522 (0.039%), neg=0, invalid=766 0324: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=766 0325: dt=36.288000, rms=0.522 (0.058%), neg=0, invalid=766 0326: dt=36.288000, rms=0.521 (0.085%), neg=0, invalid=766 0327: dt=36.288000, rms=0.521 (0.066%), neg=0, invalid=766 0328: dt=36.288000, rms=0.521 (0.044%), neg=0, invalid=766 0329: dt=36.288000, rms=0.520 (0.041%), neg=0, invalid=766 0330: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0331: dt=36.288000, rms=0.520 (0.046%), neg=0, invalid=766 0332: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0333: dt=36.288000, rms=0.519 (0.056%), neg=0, invalid=766 0334: dt=36.288000, rms=0.519 (0.055%), neg=0, invalid=766 0335: dt=36.288000, rms=0.519 (0.053%), neg=0, invalid=766 0336: dt=36.288000, rms=0.518 (0.052%), neg=0, invalid=766 0337: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0338: dt=36.288000, rms=0.518 (0.042%), neg=0, invalid=766 0339: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0340: dt=36.288000, rms=0.518 (0.047%), neg=0, invalid=766 0341: dt=36.288000, rms=0.517 (0.046%), neg=0, invalid=766 0342: dt=36.288000, rms=0.517 (0.035%), neg=0, invalid=766 0343: dt=36.288000, rms=0.517 (0.036%), neg=0, invalid=766 0344: dt=36.288000, rms=0.517 (0.033%), neg=0, invalid=766 0345: dt=36.288000, rms=0.517 (0.031%), neg=0, invalid=766 0346: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0347: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0348: dt=36.288000, rms=0.516 (0.038%), neg=0, invalid=766 0349: dt=36.288000, rms=0.516 (0.033%), neg=0, invalid=766 0350: dt=36.288000, rms=0.516 (0.034%), neg=0, invalid=766 0351: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0352: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0353: dt=36.288000, rms=0.515 (0.027%), neg=0, invalid=766 0354: dt=36.288000, rms=0.515 (0.032%), neg=0, invalid=766 0355: dt=36.288000, rms=0.515 (0.036%), neg=0, invalid=766 0356: dt=36.288000, rms=0.515 (0.031%), neg=0, invalid=766 0357: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0358: dt=36.288000, rms=0.515 (0.022%), neg=0, invalid=766 0359: dt=36.288000, rms=0.514 (0.028%), neg=0, invalid=766 0360: dt=36.288000, rms=0.514 (0.026%), neg=0, invalid=766 0361: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0362: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0363: dt=36.288000, rms=0.514 (0.024%), neg=0, invalid=766 0364: dt=124.416000, rms=0.514 (0.012%), neg=0, invalid=766 0365: dt=124.416000, rms=0.514 (-0.159%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 0366: dt=20.227979, rms=0.525 (0.130%), neg=0, invalid=766 0367: dt=31.326316, rms=0.524 (0.190%), neg=0, invalid=766 0368: dt=12.972973, rms=0.523 (0.137%), neg=0, invalid=766 0369: dt=59.508772, rms=0.522 (0.302%), neg=0, invalid=766 0370: dt=13.479452, rms=0.521 (0.263%), neg=0, invalid=766 0371: dt=179.200000, rms=0.517 (0.721%), neg=0, invalid=766 0372: dt=24.457539, rms=0.514 (0.537%), neg=0, invalid=766 0373: dt=21.157025, rms=0.513 (0.170%), neg=0, invalid=766 0374: dt=38.303030, rms=0.512 (0.170%), neg=0, invalid=766 0375: dt=11.200000, rms=0.512 (0.098%), neg=0, invalid=766 0376: dt=44.800000, rms=0.511 (0.160%), neg=0, invalid=766 0377: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=766 0378: dt=38.400000, rms=0.510 (0.132%), neg=0, invalid=766 0379: dt=11.200000, rms=0.509 (0.068%), neg=0, invalid=766 0380: dt=25.600000, rms=0.509 (0.079%), neg=0, invalid=766 0381: dt=11.200000, rms=0.509 (0.048%), neg=0, invalid=766 0382: dt=11.200000, rms=0.509 (0.055%), neg=0, invalid=766 0383: dt=11.200000, rms=0.508 (0.066%), neg=0, invalid=766 0384: dt=11.200000, rms=0.508 (0.092%), neg=0, invalid=766 0385: dt=11.200000, rms=0.507 (0.109%), neg=0, invalid=766 0386: dt=11.200000, rms=0.506 (0.139%), neg=0, invalid=766 0387: dt=11.200000, rms=0.506 (0.146%), neg=0, invalid=766 0388: dt=11.200000, rms=0.505 (0.155%), neg=0, invalid=766 0389: dt=11.200000, rms=0.504 (0.151%), neg=0, invalid=766 0390: dt=11.200000, rms=0.503 (0.168%), neg=0, invalid=766 0391: dt=11.200000, rms=0.503 (0.165%), neg=0, invalid=766 0392: dt=11.200000, rms=0.502 (0.158%), neg=0, invalid=766 0393: dt=11.200000, rms=0.501 (0.146%), neg=0, invalid=766 0394: dt=11.200000, rms=0.500 (0.133%), neg=0, invalid=766 0395: dt=11.200000, rms=0.500 (0.140%), neg=0, invalid=766 0396: dt=11.200000, rms=0.499 (0.132%), neg=0, invalid=766 0397: dt=11.200000, rms=0.498 (0.118%), neg=0, invalid=766 0398: dt=11.200000, rms=0.498 (0.112%), neg=0, invalid=766 0399: dt=11.200000, rms=0.497 (0.116%), neg=0, invalid=766 0400: dt=11.200000, rms=0.497 (0.105%), neg=0, invalid=766 0401: dt=11.200000, rms=0.496 (0.097%), neg=0, invalid=766 0402: dt=11.200000, rms=0.496 (0.083%), neg=0, invalid=766 0403: dt=11.200000, rms=0.495 (0.089%), neg=0, invalid=766 0404: dt=11.200000, rms=0.495 (0.084%), neg=0, invalid=766 0405: dt=11.200000, rms=0.495 (0.074%), neg=0, invalid=766 0406: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0407: dt=11.200000, rms=0.494 (0.060%), neg=0, invalid=766 0408: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0409: dt=11.200000, rms=0.493 (0.054%), neg=0, invalid=766 0410: dt=11.200000, rms=0.493 (0.053%), neg=0, invalid=766 0411: dt=11.200000, rms=0.493 (0.040%), neg=0, invalid=766 0412: dt=11.200000, rms=0.493 (0.051%), neg=0, invalid=766 0413: dt=11.200000, rms=0.493 (0.041%), neg=0, invalid=766 0414: dt=11.200000, rms=0.492 (0.040%), neg=0, invalid=766 0415: dt=11.200000, rms=0.492 (0.035%), neg=0, invalid=766 0416: dt=11.200000, rms=0.492 (0.041%), neg=0, invalid=766 0417: dt=11.200000, rms=0.492 (0.045%), neg=0, invalid=766 0418: dt=11.200000, rms=0.492 (0.031%), neg=0, invalid=766 0419: dt=11.200000, rms=0.491 (0.026%), neg=0, invalid=766 0420: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0421: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0422: dt=11.200000, rms=0.491 (0.023%), neg=0, invalid=766 0423: dt=11.200000, rms=0.491 (0.019%), neg=0, invalid=766 0424: dt=25.600000, rms=0.491 (0.018%), neg=0, invalid=766 0425: dt=25.600000, rms=0.491 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=766 0426: dt=28.444444, rms=0.490 (0.167%), neg=0, invalid=766 0427: dt=12.000000, rms=0.490 (0.084%), neg=0, invalid=766 0428: dt=9.600000, rms=0.489 (0.017%), neg=0, invalid=766 0429: dt=9.600000, rms=0.489 (0.022%), neg=0, invalid=766 0430: dt=9.600000, rms=0.489 (0.014%), neg=0, invalid=766 0431: dt=9.600000, rms=0.489 (0.005%), neg=0, invalid=766 0432: dt=25.600000, rms=0.489 (0.013%), neg=0, invalid=766 0433: dt=4.000000, rms=0.489 (0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0434: dt=0.000000, rms=0.519 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0435: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=766 0436: dt=1.963333, rms=0.567 (1.560%), neg=0, invalid=766 0437: dt=0.525000, rms=0.567 (0.074%), neg=0, invalid=766 0438: dt=0.448000, rms=0.567 (0.019%), neg=0, invalid=766 0439: dt=0.448000, rms=0.567 (-0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=766 0440: dt=1.282051, rms=0.566 (0.177%), neg=0, invalid=766 0441: dt=0.448000, rms=0.565 (0.014%), neg=0, invalid=766 0442: dt=0.448000, rms=0.565 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 0443: dt=0.448000, rms=0.502 (2.666%), neg=0, invalid=766 0444: dt=0.448000, rms=0.499 (0.609%), neg=0, invalid=766 0445: dt=0.448000, rms=0.497 (0.408%), neg=0, invalid=766 0446: dt=0.448000, rms=0.495 (0.275%), neg=0, invalid=766 0447: dt=0.448000, rms=0.494 (0.209%), neg=0, invalid=766 0448: dt=0.448000, rms=0.493 (0.162%), neg=0, invalid=766 0449: dt=0.028000, rms=0.493 (0.007%), neg=0, invalid=766 0450: dt=0.028000, rms=0.493 (0.009%), neg=0, invalid=766 0451: dt=0.028000, rms=0.493 (0.015%), neg=0, invalid=766 0452: dt=0.028000, rms=0.493 (0.023%), neg=0, invalid=766 0453: dt=0.028000, rms=0.493 (0.028%), neg=0, invalid=766 0454: dt=0.028000, rms=0.493 (0.031%), neg=0, invalid=766 0455: dt=0.028000, rms=0.493 (0.037%), neg=0, invalid=766 0456: dt=0.028000, rms=0.492 (0.038%), neg=0, invalid=766 0457: dt=0.028000, rms=0.492 (0.039%), neg=0, invalid=766 0458: dt=0.028000, rms=0.492 (0.043%), neg=0, invalid=766 0459: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0460: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0461: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0462: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0463: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0464: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0465: dt=0.028000, rms=0.491 (0.039%), neg=0, invalid=766 0466: dt=0.028000, rms=0.490 (0.039%), neg=0, invalid=766 0467: dt=0.028000, rms=0.490 (0.036%), neg=0, invalid=766 0468: dt=0.028000, rms=0.490 (0.002%), neg=0, invalid=766 0469: dt=0.028000, rms=0.490 (0.004%), neg=0, invalid=766 0470: dt=0.028000, rms=0.490 (0.006%), neg=0, invalid=766 0471: dt=0.028000, rms=0.490 (0.008%), neg=0, invalid=766 0472: dt=0.028000, rms=0.490 (0.007%), neg=0, invalid=766 0473: dt=0.461538, rms=0.490 (0.033%), neg=0, invalid=766 0474: dt=0.024000, rms=0.490 (0.001%), neg=0, invalid=766 0475: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0476: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0477: dt=0.024000, rms=0.490 (0.004%), neg=0, invalid=766 0478: dt=0.024000, rms=0.490 (0.005%), neg=0, invalid=766 0479: dt=0.024000, rms=0.490 (0.006%), neg=0, invalid=766 0480: dt=0.024000, rms=0.490 (0.007%), neg=0, invalid=766 0481: dt=0.024000, rms=0.490 (0.008%), neg=0, invalid=766 0482: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0483: dt=0.024000, rms=0.490 (0.009%), neg=0, invalid=766 0484: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0485: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0486: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0487: dt=0.024000, rms=0.489 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=766 0488: dt=0.384000, rms=0.486 (0.728%), neg=0, invalid=766 0489: dt=0.028000, rms=0.486 (0.009%), neg=0, invalid=766 0490: dt=0.028000, rms=0.486 (0.010%), neg=0, invalid=766 0491: dt=0.028000, rms=0.486 (0.017%), neg=0, invalid=766 0492: dt=0.028000, rms=0.486 (0.024%), neg=0, invalid=766 0493: dt=0.028000, rms=0.485 (0.027%), neg=0, invalid=766 0494: dt=0.028000, rms=0.485 (0.030%), neg=0, invalid=766 0495: dt=0.028000, rms=0.485 (0.029%), neg=0, invalid=766 0496: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=766 0497: dt=0.028000, rms=0.485 (0.026%), neg=0, invalid=766 0498: dt=0.028000, rms=0.485 (0.024%), neg=0, invalid=766 0499: dt=0.028000, rms=0.485 (0.018%), neg=0, invalid=766 0500: dt=0.000000, rms=0.485 (-0.001%), neg=0, invalid=766 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... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 0501: dt=73.984000, rms=0.483 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=766 0502: dt=129.472000, rms=0.482 (0.113%), neg=0, invalid=766 0503: dt=221.952000, rms=0.482 (0.068%), neg=0, invalid=766 0504: dt=129.472000, rms=0.481 (0.056%), neg=0, invalid=766 0505: dt=110.976000, rms=0.481 (0.027%), neg=0, invalid=766 0506: dt=110.976000, rms=0.481 (0.030%), neg=0, invalid=766 0507: dt=110.976000, rms=0.481 (0.041%), neg=0, invalid=766 0508: dt=110.976000, rms=0.481 (0.053%), neg=0, invalid=766 0509: dt=110.976000, rms=0.481 (0.049%), neg=0, invalid=766 0510: dt=110.976000, rms=0.480 (0.059%), neg=0, invalid=766 0511: dt=110.976000, rms=0.480 (0.053%), neg=0, invalid=766 0512: dt=110.976000, rms=0.480 (0.054%), neg=0, invalid=766 0513: dt=110.976000, rms=0.480 (0.049%), neg=0, invalid=766 0514: dt=110.976000, rms=0.479 (0.049%), neg=0, invalid=766 0515: dt=110.976000, rms=0.479 (0.047%), neg=0, invalid=766 0516: dt=110.976000, rms=0.479 (0.044%), neg=0, invalid=766 0517: dt=110.976000, rms=0.479 (0.043%), neg=0, invalid=766 0518: dt=110.976000, rms=0.478 (0.037%), neg=0, invalid=766 0519: dt=110.976000, rms=0.478 (0.036%), neg=0, invalid=766 0520: dt=110.976000, rms=0.478 (0.031%), neg=0, invalid=766 0521: dt=110.976000, rms=0.478 (0.030%), neg=0, invalid=766 0522: dt=110.976000, rms=0.478 (0.028%), neg=0, invalid=766 0523: dt=110.976000, rms=0.478 (0.025%), neg=0, invalid=766 0524: dt=110.976000, rms=0.478 (0.022%), neg=0, invalid=766 0525: dt=443.904000, rms=0.478 (0.005%), neg=0, invalid=766 0526: dt=443.904000, rms=0.478 (-0.062%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 0527: dt=38.588235, rms=0.477 (0.078%), neg=0, invalid=766 0528: dt=103.680000, rms=0.477 (0.118%), neg=0, invalid=766 0529: dt=145.152000, rms=0.475 (0.331%), neg=0, invalid=766 0530: dt=36.288000, rms=0.475 (0.018%), neg=0, invalid=766 0531: dt=36.288000, rms=0.475 (0.035%), neg=0, invalid=766 0532: dt=36.288000, rms=0.475 (0.064%), neg=0, invalid=766 0533: dt=36.288000, rms=0.474 (0.087%), neg=0, invalid=766 0534: dt=36.288000, rms=0.474 (0.100%), neg=0, invalid=766 0535: dt=18.144000, rms=0.474 (0.019%), neg=0, invalid=766 0536: dt=9.072000, rms=0.474 (0.010%), neg=0, invalid=766 0537: dt=6.480000, rms=0.474 (0.007%), neg=0, invalid=766 0538: dt=0.101250, rms=0.474 (0.000%), neg=0, invalid=766 0539: dt=0.025312, rms=0.474 (0.000%), neg=0, invalid=766 0540: dt=0.012656, rms=0.474 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 0541: dt=132.512821, rms=0.471 (0.546%), neg=0, invalid=766 0542: dt=44.800000, rms=0.470 (0.141%), neg=0, invalid=766 0543: dt=103.680000, rms=0.470 (0.116%), neg=0, invalid=766 0544: dt=414.720000, rms=0.468 (0.287%), neg=0, invalid=766 0545: dt=43.000000, rms=0.468 (0.096%), neg=0, invalid=766 0546: dt=36.288000, rms=0.468 (0.019%), neg=0, invalid=766 0547: dt=36.288000, rms=0.468 (0.017%), neg=0, invalid=766 0548: dt=18.144000, rms=0.468 (0.008%), neg=0, invalid=766 0549: dt=9.072000, rms=0.468 (0.004%), neg=0, invalid=766 0550: dt=9.072000, rms=0.468 (0.005%), neg=0, invalid=766 0551: dt=0.567000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 0552: dt=11.200000, rms=0.467 (0.281%), neg=0, invalid=766 0553: dt=0.700000, rms=0.467 (0.016%), neg=0, invalid=766 0554: dt=0.350000, rms=0.467 (0.008%), neg=0, invalid=766 0555: dt=0.175000, rms=0.467 (0.004%), neg=0, invalid=766 0556: dt=0.021875, rms=0.467 (0.000%), neg=0, invalid=766 0557: dt=0.000684, rms=0.467 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0558: dt=44.800000, rms=0.462 (1.098%), neg=0, invalid=766 0559: dt=44.800000, rms=0.459 (0.606%), neg=0, invalid=766 0560: dt=38.400000, rms=0.457 (0.489%), neg=0, invalid=766 0561: dt=44.800000, rms=0.456 (0.222%), neg=0, invalid=766 0562: dt=11.200000, rms=0.455 (0.147%), neg=0, invalid=766 0563: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0564: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0565: dt=0.043750, rms=0.455 (0.000%), neg=0, invalid=766 0566: dt=0.005469, rms=0.455 (0.000%), neg=0, invalid=766 0567: dt=0.000684, rms=0.455 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0568: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0569: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 0570: dt=0.906250, rms=0.465 (0.232%), neg=0, invalid=766 0571: dt=0.448000, rms=0.464 (0.065%), neg=0, invalid=766 0572: dt=0.681818, rms=0.464 (0.070%), neg=0, invalid=766 0573: dt=1.792000, rms=0.464 (0.057%), neg=0, invalid=766 0574: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 0575: dt=0.100000, rms=0.464 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0576: dt=1.536000, rms=0.463 (0.243%), neg=0, invalid=766 0577: dt=0.541667, rms=0.462 (0.043%), neg=0, invalid=766 0578: dt=0.541667, rms=0.462 (0.036%), neg=0, invalid=766 0579: dt=0.541667, rms=0.462 (0.056%), neg=0, invalid=766 0580: dt=0.541667, rms=0.462 (0.018%), neg=0, invalid=766 0581: dt=0.541667, rms=0.462 (0.027%), neg=0, invalid=766 0582: dt=0.541667, rms=0.462 (0.024%), neg=0, invalid=766 0583: dt=0.541667, rms=0.462 (0.010%), neg=0, invalid=766 0584: dt=0.000000, rms=0.462 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 0585: dt=0.140550, rms=0.451 (0.763%), neg=0, invalid=766 0586: dt=0.122596, rms=0.449 (0.477%), neg=0, invalid=766 0587: dt=0.112257, rms=0.448 (0.334%), neg=0, invalid=766 0588: dt=0.112000, rms=0.447 (0.265%), neg=0, invalid=766 0589: dt=0.112000, rms=0.446 (0.214%), neg=0, invalid=766 0590: dt=0.112000, rms=0.445 (0.174%), neg=0, invalid=766 0591: dt=0.112000, rms=0.444 (0.144%), neg=0, invalid=766 0592: dt=0.112000, rms=0.444 (0.120%), neg=0, invalid=766 0593: dt=0.112000, rms=0.443 (0.101%), neg=0, invalid=766 0594: dt=0.112000, rms=0.443 (0.086%), neg=0, invalid=766 0595: dt=0.112000, rms=0.442 (0.074%), neg=0, invalid=766 0596: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0597: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0598: dt=0.028000, rms=0.442 (0.029%), neg=0, invalid=766 0599: dt=0.028000, rms=0.442 (0.040%), neg=0, invalid=766 0600: dt=0.028000, rms=0.442 (0.049%), neg=0, invalid=766 0601: dt=0.028000, rms=0.442 (0.011%), neg=0, invalid=766 0602: dt=0.028000, rms=0.442 (0.021%), neg=0, invalid=766 0603: dt=0.028000, rms=0.442 (0.030%), neg=0, invalid=766 0604: dt=0.028000, rms=0.441 (0.037%), neg=0, invalid=766 0605: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0606: dt=0.028000, rms=0.441 (0.045%), neg=0, invalid=766 0607: dt=0.028000, rms=0.441 (0.007%), neg=0, invalid=766 0608: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0609: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0610: dt=0.112000, rms=0.441 (0.025%), neg=0, invalid=766 0611: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0612: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0613: dt=0.028000, rms=0.441 (0.011%), neg=0, invalid=766 0614: dt=0.028000, rms=0.441 (0.015%), neg=0, invalid=766 0615: dt=0.028000, rms=0.441 (0.018%), neg=0, invalid=766 0616: dt=0.028000, rms=0.440 (0.021%), neg=0, invalid=766 0617: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 0618: dt=0.028000, rms=0.440 (0.008%), neg=0, invalid=766 0619: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=766 0620: dt=0.028000, rms=0.440 (0.058%), neg=0, invalid=766 0621: dt=0.028000, rms=0.440 (0.054%), neg=0, invalid=766 0622: dt=0.024000, rms=0.440 (0.043%), neg=0, invalid=766 0623: dt=0.024000, rms=0.439 (0.041%), neg=0, invalid=766 0624: dt=0.024000, rms=0.439 (0.075%), neg=0, invalid=766 0625: dt=0.024000, rms=0.439 (0.035%), neg=0, invalid=766 0626: dt=0.024000, rms=0.439 (0.064%), neg=0, invalid=766 0627: dt=0.024000, rms=0.438 (0.086%), neg=0, invalid=766 0628: dt=0.024000, rms=0.438 (0.101%), neg=0, invalid=766 0629: dt=0.024000, rms=0.437 (0.108%), neg=0, invalid=766 0630: dt=0.024000, rms=0.437 (0.109%), neg=0, invalid=766 0631: dt=0.024000, rms=0.436 (0.104%), neg=0, invalid=766 0632: dt=0.024000, rms=0.436 (0.095%), neg=0, invalid=766 0633: dt=0.024000, rms=0.436 (0.082%), neg=0, invalid=766 0634: dt=0.024000, rms=0.435 (0.068%), neg=0, invalid=766 0635: dt=0.024000, rms=0.435 (0.053%), neg=0, invalid=766 0636: dt=0.024000, rms=0.435 (0.038%), neg=0, invalid=766 0637: dt=0.024000, rms=0.435 (0.023%), neg=0, invalid=766 0638: dt=0.024000, rms=0.435 (0.009%), neg=0, invalid=766 0639: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 4 hours, 9 minutes and 13 seconds. #-------------------------------------- #@# CA Reg Inv Wed Mar 3 20:50:02 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Mar 3 20:51:02 CET 2010
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11104963 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA Wed Mar 3 20:52:16 CET 2010
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.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 '/home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (45, 52, 28) --> (207, 202, 237) using (99, 102, 133) as brain centroid... mean wm in atlas = 126, using box (79,84,107) --> (118, 120,158) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 140, scaling input intensities by 0.900 scaling channel 0 by 0.9
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-17103.0 (thresh=-17085.9) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-14667.9 (thresh=-14653.3) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14488.4, old_max_log_p =-14667.9 (thresh=-14653.3) 1.036 -0.063 -0.081 14.725; 0.070 1.213 0.222 -79.106; 0.083 -0.208 0.964 -0.991; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14488.4 (thresh=-14473.9) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14436.8 (thresh=-14422.4) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14436.8 (thresh=-14422.4) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14336.6 (thresh=-14322.3) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 3481 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 14336.6 tol 0.000010 Resulting transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -14336.6 (old=-17103.0) transform before final EM align: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 382743 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1833208.1 tol 0.000000 final transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta... registration took 49 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Wed Mar 3 21:42:15 CET 2010
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
$Id: mri_seg_diff.c,v 1.3.2.1 2008/09/03 22:02:00 nicks Exp $ cwd /home/kutato/freesurfer/subjects/C1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname localhost.localdomain machine x86_64 user kutato Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmenations No difference found.
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /home/kutato/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /home/kutato/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, overlap=0.688) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, peak = 32), gca=32.4 gca peak = 0.14982 (20) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, overlap=0.231) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, peak = 28), gca=28.5 gca peak = 0.28003 (97) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, peak = 102), gca=101.8 gca peak = 0.18160 (96) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, overlap=0.407) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, peak = 78), gca=77.5 gca peak = 0.32745 (63) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, peak = 77), gca=77.2 gca peak = 0.08597 (105) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, overlap=0.045) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, peak = 80), gca=80.3 gca peak = 0.08598 (64) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, overlap=0.074) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, peak = 85), gca=85.2 gca peak = 0.18227 (75) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, overlap=0.228) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, peak = 84), gca=84.4 gca peak = 0.10629 (62) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, peak = 85), gca=85.2 gca peak = 0.11668 (59) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, peak = 83), gca=82.6 gca peak = 0.17849 (88) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, peak = 112), gca=112.2 gca peak = 0.16819 (86) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, peak = 108), gca=107.5 gca peak = 0.41688 (64) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, peak = 80), gca=80.0 gca peak = 0.42394 (62) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, peak = 81), gca=80.6 gca peak = 0.10041 (96) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, overlap=0.774) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, overlap=0.443) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, overlap=0.331) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, peak = 91), gca=91.1 gca peak = 0.09624 (82) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, overlap=0.394) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, overlap=0.000) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, peak = 103), gca=103.4 gca peak = 0.12757 (95) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, overlap=0.525) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, overlap=0.902) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, peak = 32), gca=32.4 gca peak = 0.26069 (23) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, overlap=0.240) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.23 x + 0.0 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14396 (33) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, overlap=0.871) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, peak = 31), gca=31.4 gca peak = 0.13467 (29) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, overlap=0.673) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, peak = 31), gca=31.2 gca peak = 0.27948 (102) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, peak = 102), gca=102.0 gca peak = 0.18507 (101) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, peak = 101), gca=101.0 gca peak = 0.21463 (78) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, peak = 76), gca=76.1 gca peak = 0.27122 (77) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 77), gca=77.0 gca peak = 0.08007 (112) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, overlap=0.810) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, peak = 112), gca=112.0 gca peak = 0.08789 (111) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, overlap=0.795) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, peak = 114), gca=113.8 gca peak = 0.06240 (80) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, overlap=0.591) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, peak = 78), gca=78.0 gca peak = 0.07094 (77) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, overlap=0.711) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, peak = 75), gca=75.1 gca peak = 0.23769 (85) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, peak = 85), gca=85.0 gca peak = 0.13104 (84) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, overlap=0.845) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, peak = 86), gca=86.1 gca peak = 0.08141 (85) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, overlap=0.690) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, peak = 83), gca=82.9 gca peak = 0.09212 (83) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, overlap=0.736) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, peak = 83), gca=83.0 gca peak = 0.14004 (112) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, overlap=0.965) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, peak = 112), gca=112.0 gca peak = 0.13912 (108) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, peak = 108), gca=108.0 gca peak = 0.30905 (79) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 81), gca=81.0 gca peak = 0.37870 (81) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, peak = 79), gca=79.0 gca peak = 0.10116 (99) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, overlap=0.963) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, peak = 99), gca=99.0 gca peak = 0.09774 (97) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, overlap=0.918) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, peak = 97), gca=97.0 gca peak = 0.08941 (98) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, peak = 98), gca=98.0 gca peak = 0.08263 (85) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, overlap=0.828) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, peak = 85), gca=85.0 gca peak = 0.06255 (104) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, overlap=0.638) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, peak = 104), gca=104.0 gca peak = 0.14189 (104) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, overlap=0.808) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, peak = 104), gca=104.0 gca peak = 0.16147 (99) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, peak = 99), gca=99.0 gca peak = 0.22647 (34) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, overlap=0.851) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, peak = 33), gca=33.2 gca peak = 0.16050 (32) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, overlap=0.781) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, peak = 32), gca=32.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26758 (43) gca peak CSF = 0.17739 (47) gca peak Left_Accumbens_area = 0.36131 (79) gca peak Left_undetermined = 0.95107 (38) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.22906 (40) gca peak Right_Accumbens_area = 0.27742 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.12959 (48) gca peak Fifth_Ventricle = 0.50102 (51) gca peak WM_hypointensities = 0.15008 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34132 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 33062 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 306 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77084 changed. image ll: -2.213, PF=1.000 pass 2: 12120 changed. image ll: -2.211, PF=1.000 pass 3: 4101 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 30 minutes and 38 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz C1
reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /home/kutato/freesurfer/subjects/C1/mri/aseg.auto_noCCseg.mgz reading norm from /home/kutato/freesurfer/subjects/C1/mri/norm.mgz 44494 voxels in left wm, 85128 in right wm, xrange [115, 131] global minimum found at slice 125.0, rotations (-3.75, -0.25) final transformation (x=125.0, yr=-3.750, zr=-0.250): 0.998 0.004 -0.065 11.082; -0.004 1.000 0.000 0.509; 0.065 0.000 0.998 -7.901; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 133 113 eigenvectors: -0.002 -0.003 1.000; -0.035 -0.999 -0.003; 0.999 -0.035 0.002; error in mid anterior detected - correcting... writing aseg with callosum to to /home/kutato/freesurfer/subjects/C1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.8 minutes #-------------------------------------- #@# Merge ASeg Wed Mar 3 22:14:45 CET 2010
cp aseg.auto.mgz aseg.mgz
#-------------------------------------------- #@# Intensity Normalization2 Wed Mar 3 22:14:45 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using control points from file /home/kutato/freesurfer/subjects/C1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 710 control points... only using 710 control points from file... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 223389 control points removed building Voronoi diagram... performing soap bubble smoothing... 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 brain.mgz 3D bias adjustment took 6 minutes and 6 seconds. using MR volume brainmask.mgz to mask input volume... using wm (255) threshold 245.0 for removing exterior voxels white matter peak found at 111 gm peak at 77 (77), valley at 40 (40) csf peak at 28, setting threshold to 60 white matter peak found at 111 gm peak at 78 (78), valley at 40 (40) csf peak at 29, setting threshold to 61 #-------------------------------------------- #@# Mask BFS Wed Mar 3 22:20:55 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Mar 3 22:20:58 CET 2010
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (109.0): 107.5 +- 7.5 [80.0 --> 125.0] GM (68.0) : 65.0 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10488 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4151 filled 110391 bright non-wm voxels segmented. 7168 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz...
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume... auto filling took 0.76 minutes reading wm segmentation from wm.seg.mgz... 404 voxels added to wm to prevent paths from MTL structures to cortex 6112 additional wm voxels added 0 additional wm voxels added SEG EDIT: 68648 voxels turned on, 46182 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 90 new 90 115,126,128 old 90 new 90 writing edited volume to wm.asegedit.mgz....
mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1 pass 1 (xy+): 154 found - 154 modified | TOTAL: 154 pass 2 (xy+): 0 found - 154 modified | TOTAL: 154 pass 1 (xy-): 134 found - 134 modified | TOTAL: 288 pass 2 (xy-): 0 found - 134 modified | TOTAL: 288 pass 1 (yz+): 124 found - 124 modified | TOTAL: 412 pass 2 (yz+): 0 found - 124 modified | TOTAL: 412 pass 1 (yz-): 99 found - 99 modified | TOTAL: 511 pass 2 (yz-): 0 found - 99 modified | TOTAL: 511 pass 1 (xz+): 137 found - 137 modified | TOTAL: 648 pass 2 (xz+): 0 found - 137 modified | TOTAL: 648 pass 1 (xz-): 124 found - 124 modified | TOTAL: 772 pass 2 (xz-): 0 found - 124 modified | TOTAL: 772 Iteration Number : 1 pass 1 (+++): 100 found - 100 modified | TOTAL: 100 pass 2 (+++): 0 found - 100 modified | TOTAL: 100 pass 1 (+++): 97 found - 97 modified | TOTAL: 197 pass 2 (+++): 0 found - 97 modified | TOTAL: 197 pass 1 (+++): 84 found - 84 modified | TOTAL: 281 pass 2 (+++): 0 found - 84 modified | TOTAL: 281 pass 1 (+++): 135 found - 135 modified | TOTAL: 416 pass 2 (+++): 0 found - 135 modified | TOTAL: 416 Iteration Number : 1 pass 1 (++): 141 found - 141 modified | TOTAL: 141 pass 2 (++): 0 found - 141 modified | TOTAL: 141 pass 1 (+-): 205 found - 205 modified | TOTAL: 346 pass 2 (+-): 0 found - 205 modified | TOTAL: 346 pass 1 (--): 152 found - 152 modified | TOTAL: 498 pass 2 (--): 1 found - 153 modified | TOTAL: 499 pass 3 (--): 0 found - 153 modified | TOTAL: 499 pass 1 (-+): 183 found - 183 modified | TOTAL: 682 pass 2 (-+): 0 found - 183 modified | TOTAL: 682 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 23 found - 23 modified | TOTAL: 45 pass 2 (xy-): 0 found - 23 modified | TOTAL: 45 pass 1 (yz+): 19 found - 19 modified | TOTAL: 64 pass 2 (yz+): 0 found - 19 modified | TOTAL: 64 pass 1 (yz-): 37 found - 37 modified | TOTAL: 101 pass 2 (yz-): 0 found - 37 modified | TOTAL: 101 pass 1 (xz+): 39 found - 39 modified | TOTAL: 140 pass 2 (xz+): 0 found - 39 modified | TOTAL: 140 pass 1 (xz-): 22 found - 22 modified | TOTAL: 162 pass 2 (xz-): 0 found - 22 modified | TOTAL: 162 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 pass 1 (+++): 4 found - 4 modified | TOTAL: 19 pass 2 (+++): 0 found - 4 modified | TOTAL: 19 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 22 found - 22 modified | TOTAL: 35 pass 2 (+-): 0 found - 22 modified | TOTAL: 35 pass 1 (--): 17 found - 17 modified | TOTAL: 52 pass 2 (--): 0 found - 17 modified | TOTAL: 52 pass 1 (-+): 10 found - 10 modified | TOTAL: 62 pass 2 (-+): 0 found - 10 modified | TOTAL: 62 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 2131 (out of 674704: 0.315842) keeping edits binarizing input wm segmentation... Ambiguous edge configurations...
Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels
mri_pretess done
#-------------------------------------------- #@# Fill Wed Mar 3 22:23:31 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 619 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 119, 151), TAL = (2.0, 23.0, 9.0) talairach voxel to voxel transform 0.943 0.014 0.050 -0.471; -0.002 0.809 -0.158 52.074; -0.063 0.140 0.999 12.198; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 119, 151) --> (2.0, 23.0, 9.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 23.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 9.00) SRC: (110.64, 124.32, 172.81) search lh wm seed point around talairach space (-16.00, 23.00, 9.00), SRC: (144.61, 124.24, 170.53) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Mar 3 22:24:28 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 12 found - 12 modified | TOTAL: 25 pass 2 (xy-): 0 found - 12 modified | TOTAL: 25 pass 1 (yz+): 10 found - 10 modified | TOTAL: 35 pass 2 (yz+): 0 found - 10 modified | TOTAL: 35 pass 1 (yz-): 22 found - 22 modified | TOTAL: 57 pass 2 (yz-): 0 found - 22 modified | TOTAL: 57 pass 1 (xz+): 15 found - 15 modified | TOTAL: 72 pass 2 (xz+): 0 found - 15 modified | TOTAL: 72 pass 1 (xz-): 5 found - 5 modified | TOTAL: 77 pass 2 (xz-): 0 found - 5 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 9 found - 9 modified | TOTAL: 15 pass 2 (+-): 0 found - 9 modified | TOTAL: 15 pass 1 (--): 13 found - 13 modified | TOTAL: 28 pass 2 (--): 0 found - 13 modified | TOTAL: 28 pass 1 (-+): 3 found - 3 modified | TOTAL: 31 pass 2 (-+): 0 found - 3 modified | TOTAL: 31 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 128 (out of 320366: 0.039954) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ slice 50: 715 vertices, 806 faces slice 60: 6587 vertices, 6870 faces slice 70: 16362 vertices, 16829 faces slice 80: 27996 vertices, 28461 faces slice 90: 40299 vertices, 40842 faces slice 100: 52688 vertices, 53229 faces slice 110: 65001 vertices, 65581 faces slice 120: 77662 vertices, 78249 faces slice 130: 89134 vertices, 89714 faces slice 140: 100712 vertices, 101362 faces slice 150: 112906 vertices, 113608 faces slice 160: 123188 vertices, 123863 faces slice 170: 130916 vertices, 131557 faces slice 180: 137022 vertices, 137584 faces slice 190: 141777 vertices, 142325 faces slice 200: 145789 vertices, 146310 faces slice 210: 149464 vertices, 149996 faces slice 220: 152836 vertices, 153278 faces slice 230: 152952 vertices, 153360 faces slice 240: 152952 vertices, 153360 faces slice 250: 152952 vertices, 153360 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components... 152952 voxel in cpt #1: X=-408 [v=152952,e=460080,f=306720] located at (-25.554226, -6.675813, -2.117488) For the whole surface: X=-408 [v=152952,e=460080,f=306720] One single component has been found nothing to do done
#-------------------------------------------- #@# Smooth1 lh Wed Mar 3 22:24:41 CET 2010
mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/kutato/freesurfer/subjects/C1/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Mar 3 22:24:46 CET 2010
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/kutato/freesurfer/subjects/C1/scripts avg radius = 49.0 mm, total surface area = 79501 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.071 (target=0.015) step 030: RMS=0.069 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.065 (target=0.015) step 045: RMS=0.065 (target=0.015) step 050: RMS=0.065 (target=0.015) step 055: RMS=0.065 (target=0.015) step 060: RMS=0.065 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Mar 3 22:25:42 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, sigma=0.0, host=local, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90
surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.88 (0.00-->27.18) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-1.82-->2.32) tol=1.0e-01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
301: dt: 15.53, sse: 8540.7 (0.052, 34.9, 0.000), neg: 26636 (%4.389:%4.53), avgs: 32 302: dt: 0.29, sse: 8539.7 (0.052, 34.9, 0.000), neg: 26636 (%4.375:%4.52), avgs: 32 303: dt: 0.29, sse: 8538.0 (0.052, 34.9, 0.000), neg: 26627 (%4.349:%4.52), avgs: 32 304: dt: 0.29, sse: 8536.1 (0.052, 34.9, 0.000), neg: 26615 (%4.318:%4.51), avgs: 32 305: dt: 0.29, sse: 8533.4 (0.052, 34.9, 0.000), neg: 26609 (%4.275:%4.50), avgs: 32 306: dt: 0.29, sse: 8530.6 (0.052, 34.8, 0.000), neg: 26596 (%4.228:%4.49), avgs: 32 307: dt: 0.29, sse: 8527.6 (0.052, 34.8, 0.000), neg: 26579 (%4.176:%4.48), avgs: 32 308: dt: 0.29, sse: 8524.4 (0.052, 34.8, 0.000), neg: 26560 (%4.119:%4.46), avgs: 32 309: dt: 0.29, sse: 8520.9 (0.052, 34.8, 0.000), neg: 26543 (%4.058:%4.45), avgs: 32 310: dt: 0.29, sse: 8517.4 (0.051, 34.8, 0.000), neg: 26523 (%3.994:%4.43), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->25.82) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.93-->2.40) 311: dt: 0.29, sse: 8514.0 (0.051, 34.8, 0.000), neg: 26509 (%3.932:%4.41), avgs: 32 312: dt: 48.14, sse: 8479.7 (0.051, 34.6, 0.000), neg: 26094 (%3.212:%4.03), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->24.45) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.71-->2.54) 313: dt: 3.56, sse: 8469.9 (0.051, 34.7, 0.000), neg: 26269 (%2.998:%4.03), avgs: 8 314: dt: 0.15, sse: 8469.3 (0.051, 34.7, 0.000), neg: 26242 (%2.986:%4.01), avgs: 8 315: dt: 0.15, sse: 8468.6 (0.051, 34.7, 0.000), neg: 26253 (%2.969:%4.00), avgs: 8 316: dt: 0.15, sse: 8467.1 (0.051, 34.7, 0.000), neg: 26267 (%2.942:%3.99), avgs: 8 317: dt: 0.15, sse: 8466.2 (0.051, 34.7, 0.000), neg: 26292 (%2.922:%3.98), avgs: 8 318: dt: 0.15, sse: 8465.3 (0.051, 34.7, 0.000), neg: 26295 (%2.901:%3.97), avgs: 8 319: dt: 0.15, sse: 8465.2 (0.051, 34.7, 0.000), neg: 26300 (%2.890:%3.96), avgs: 8 320: dt: 0.15, sse: 8464.7 (0.051, 34.7, 0.000), neg: 26310 (%2.872:%3.95), avgs: 8 vertex spacing 0.98 +- 0.88 (0.00-->23.63) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.52-->2.61) 321: dt: 0.15, sse: 8464.2 (0.051, 34.7, 0.000), neg: 26327 (%2.854:%3.94), avgs: 8 322: dt: 0.15, sse: 8463.7 (0.051, 34.7, 0.000), neg: 26343 (%2.835:%3.93), avgs: 8 323: dt: 0.15, sse: 8462.9 (0.051, 34.7, 0.000), neg: 26359 (%2.810:%3.93), avgs: 8 324: dt: 2.69, sse: 8458.0 (0.051, 34.7, 0.000), neg: 26415 (%2.703:%3.92), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->23.23) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.47-->2.64) 325: dt: 1.44, sse: 8454.2 (0.051, 34.7, 0.000), neg: 26661 (%2.601:%3.93), avgs: 2 326: dt: 0.09, sse: 8453.8 (0.051, 34.7, 0.000), neg: 26697 (%2.581:%3.93), avgs: 2 327: dt: 0.09, sse: 8452.8 (0.051, 34.8, 0.000), neg: 26737 (%2.553:%3.93), avgs: 2 328: dt: 0.09, sse: 8451.9 (0.051, 34.8, 0.000), neg: 26779 (%2.526:%3.92), avgs: 2 329: dt: 0.09, sse: 8451.5 (0.051, 34.8, 0.000), neg: 26818 (%2.503:%3.92), avgs: 2 330: dt: 0.09, sse: 8450.9 (0.051, 34.8, 0.000), neg: 26880 (%2.480:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.65) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.26-->2.69) 331: dt: 0.09, sse: 8450.2 (0.051, 34.8, 0.000), neg: 26944 (%2.455:%3.91), avgs: 2 332: dt: 0.09, sse: 8449.5 (0.051, 34.8, 0.000), neg: 27007 (%2.430:%3.92), avgs: 2 333: dt: 0.09, sse: 8449.1 (0.051, 34.8, 0.000), neg: 27074 (%2.410:%3.91), avgs: 2 334: dt: 0.09, sse: 8448.9 (0.051, 34.9, 0.000), neg: 27156 (%2.391:%3.92), avgs: 2 335: dt: 0.09, sse: 8448.2 (0.051, 34.9, 0.000), neg: 27231 (%2.368:%3.92), avgs: 2 336: dt: 0.06, sse: 8448.1 (0.051, 34.9, 0.000), neg: 27244 (%2.366:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.33) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.39-->2.72) 337: dt: 0.16, sse: 8447.2 (0.051, 34.9, 0.000), neg: 27436 (%2.337:%3.96), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.21-->2.72) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
338: dt: 107.53, sse: 1470.7 (0.051, 34.6, 0.000), neg: 26824 (%1.951:%3.54), avgs: 32 scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.782, avgs=0 005/300: dt: 0.9000, rms radial error=177.523, avgs=0 010/300: dt: 0.9000, rms radial error=176.967, avgs=0 015/300: dt: 0.9000, rms radial error=176.237, avgs=0 020/300: dt: 0.9000, rms radial error=175.406, avgs=0 025/300: dt: 0.9000, rms radial error=174.516, avgs=0 030/300: dt: 0.9000, rms radial error=173.592, avgs=0 035/300: dt: 0.9000, rms radial error=172.654, avgs=0 040/300: dt: 0.9000, rms radial error=171.710, avgs=0 045/300: dt: 0.9000, rms radial error=170.765, avgs=0 050/300: dt: 0.9000, rms radial error=169.821, avgs=0 055/300: dt: 0.9000, rms radial error=168.881, avgs=0 060/300: dt: 0.9000, rms radial error=167.944, avgs=0 065/300: dt: 0.9000, rms radial error=167.011, avgs=0 070/300: dt: 0.9000, rms radial error=166.083, avgs=0 075/300: dt: 0.9000, rms radial error=165.160, avgs=0 080/300: dt: 0.9000, rms radial error=164.243, avgs=0 085/300: dt: 0.9000, rms radial error=163.332, avgs=0 090/300: dt: 0.9000, rms radial error=162.426, avgs=0 095/300: dt: 0.9000, rms radial error=161.525, avgs=0 100/300: dt: 0.9000, rms radial error=160.628, avgs=0 105/300: dt: 0.9000, rms radial error=159.737, avgs=0 110/300: dt: 0.9000, rms radial error=158.850, avgs=0 115/300: dt: 0.9000, rms radial error=157.968, avgs=0 120/300: dt: 0.9000, rms radial error=157.091, avgs=0 125/300: dt: 0.9000, rms radial error=156.218, avgs=0 130/300: dt: 0.9000, rms radial error=155.350, avgs=0 135/300: dt: 0.9000, rms radial error=154.488, avgs=0 140/300: dt: 0.9000, rms radial error=153.631, avgs=0 145/300: dt: 0.9000, rms radial error=152.778, avgs=0 150/300: dt: 0.9000, rms radial error=151.929, avgs=0 155/300: dt: 0.9000, rms radial error=151.086, avgs=0 160/300: dt: 0.9000, rms radial error=150.246, avgs=0 165/300: dt: 0.9000, rms radial error=149.411, avgs=0 170/300: dt: 0.9000, rms radial error=148.581, avgs=0 175/300: dt: 0.9000, rms radial error=147.754, avgs=0 180/300: dt: 0.9000, rms radial error=146.933, avgs=0 185/300: dt: 0.9000, rms radial error=146.115, avgs=0 190/300: dt: 0.9000, rms radial error=145.302, avgs=0 195/300: dt: 0.9000, rms radial error=144.493, avgs=0 200/300: dt: 0.9000, rms radial error=143.688, avgs=0 205/300: dt: 0.9000, rms radial error=142.888, avgs=0 210/300: dt: 0.9000, rms radial error=142.091, avgs=0 215/300: dt: 0.9000, rms radial error=141.299, avgs=0 220/300: dt: 0.9000, rms radial error=140.511, avgs=0 225/300: dt: 0.9000, rms radial error=139.727, avgs=0 230/300: dt: 0.9000, rms radial error=138.948, avgs=0 235/300: dt: 0.9000, rms radial error=138.172, avgs=0 240/300: dt: 0.9000, rms radial error=137.401, avgs=0 245/300: dt: 0.9000, rms radial error=136.634, avgs=0 250/300: dt: 0.9000, rms radial error=135.871, avgs=0 255/300: dt: 0.9000, rms radial error=135.112, avgs=0 260/300: dt: 0.9000, rms radial error=134.358, avgs=0 265/300: dt: 0.9000, rms radial error=133.607, avgs=0 270/300: dt: 0.9000, rms radial error=132.860, avgs=0 275/300: dt: 0.9000, rms radial error=132.118, avgs=0 280/300: dt: 0.9000, rms radial error=131.379, avgs=0 285/300: dt: 0.9000, rms radial error=130.645, avgs=0 290/300: dt: 0.9000, rms radial error=129.914, avgs=0 295/300: dt: 0.9000, rms radial error=129.188, avgs=0 300/300: dt: 0.9000, rms radial error=128.465, avgs=0
spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 8624.98 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.02/37 = 0.00056 epoch 2 (K=80.0), pass 1, starting sse = 1491.66 integrating with navgs=32 and tol=3.200e+00 taking m339: dt: 0.29, sse: 1470.4 (0.051, 34.7, 0.000), neg: 26880 (%1.943:%3.54), avgs: 32 340: dt: 0.29, sse: 1470.0 (0.051, 34.7, 0.000), neg: 26948 (%1.935:%3.54), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.68) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.75) 341: dt: 0.29, sse: 1469.7 (0.051, 34.7, 0.000), neg: 27043 (%1.927:%3.55), avgs: 32 342: dt: 0.29, sse: 1469.3 (0.051, 34.7, 0.000), neg: 27089 (%1.919:%3.55), avgs: 32 343: dt: 0.29, sse: 1468.9 (0.051, 34.7, 0.000), neg: 27143 (%1.911:%3.55), avgs: 32 344: dt: 0.29, sse: 1468.5 (0.051, 34.7, 0.000), neg: 27154 (%1.903:%3.55), avgs: 32 345: dt: 0.29, sse: 1467.9 (0.051, 34.7, 0.000), neg: 27168 (%1.892:%3.54), avgs: 32 346: dt: 0.29, sse: 1467.6 (0.051, 34.7, 0.000), neg: 27200 (%1.886:%3.53), avgs: 32 347: dt: 0.29, sse: 1467.3 (0.051, 34.7, 0.000), neg: 27216 (%1.879:%3.53), avgs: 32 348: dt: 0.29, sse: 1466.8 (0.051, 34.7, 0.000), neg: 27228 (%1.870:%3.52), avgs: 32 349: dt: 36.97, sse: 1459.2 (0.051, 34.6, 0.000), neg: 27004 (%1.742:%3.40), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.80) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.79) 350: dt: 4.85, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27064 (%1.688:%3.39), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.81) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.21-->2.79) 351: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27067 (%1.685:%3.39), avgs: 8 352: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27083 (%1.684:%3.39), avgs: 8 353: dt: 0.15, sse: 1455.9 (0.051, 34.6, 0.000), neg: 27080 (%1.681:%3.37), avgs: 8 354: dt: 0.15, sse: 1456.3 (0.051, 34.6, 0.000), neg: 27102 (%1.684:%3.38), avgs: 8 355: dt: 0.15, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27124 (%1.681:%3.37), avgs: 8 356: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27155 (%1.679:%3.37), avgs: 8 357: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27182 (%1.677:%3.36), avgs: 8 358: dt: 0.15, sse: 1456.0 (0.051, 34.6, 0.000), neg: 27190 (%1.674:%3.36), avgs: 8 359: dt: 0.15, sse: 1455.8 (0.051, 34.6, 0.000), neg: 27194 (%1.669:%3.35), avgs: 8 360: dt: 0.15, sse: 1455.6 (0.051, 34.6, 0.000), neg: 27210 (%1.665:%3.35), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.92) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.80) 361: dt: 9.20, sse: 1452.7 (0.051, 34.6, 0.000), neg: 27182 (%1.611:%3.30), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.00) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.80) 362: dt: 0.77, sse: 1451.0 (0.051, 34.6, 0.000), neg: 27300 (%1.582:%3.32), avgs: 2 363: dt: 0.09, sse: 1450.6 (0.051, 34.6, 0.000), neg: 27301 (%1.575:%3.31), avgs: 2 364: dt: 0.09, sse: 1450.3 (0.051, 34.6, 0.000), neg: 27336 (%1.568:%3.31), avgs: 2 365: dt: 0.09, sse: 1449.7 (0.051, 34.6, 0.000), neg: 27352 (%1.556:%3.31), avgs: 2 366: dt: 0.09, sse: 1449.0 (0.051, 34.6, 0.000), neg: 27377 (%1.544:%3.32), avgs: 2 367: dt: 0.09, sse: 1448.6 (0.051, 34.6, 0.000), neg: 27398 (%1.536:%3.31), avgs: 2 368: dt: 0.09, sse: 1448.0 (0.051, 34.6, 0.000), neg: 27412 (%1.526:%3.31), avgs: 2 369: dt: 0.09, sse: 1447.4 (0.051, 34.6, 0.000), neg: 27438 (%1.514:%3.30), avgs: 2 370: dt: 0.09, sse: 1446.5 (0.051, 34.6, 0.000), neg: 27458 (%1.499:%3.30), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.08) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.14-->2.80) 371: dt: 0.09, sse: 1445.8 (0.051, 34.6, 0.000), neg: 27460 (%1.486:%3.29), avgs: 2 372: dt: 0.09, sse: 1445.1 (0.051, 34.6, 0.000), neg: 27497 (%1.474:%3.28), avgs: 2 373: dt: 1.48, sse: 1443.8 (0.051, 34.7, 0.000), neg: 27589 (%1.452:%3.29), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.12-->2.81) 374: dt: 0.27, sse: 1443.2 (0.051, 34.7, 0.000), neg: 27714 (%1.439:%3.27), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.29-->2.81) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
375: dt: 36.63, sse: 250.8 (0.051, 34.6, 0.000), neg: 27421 (%1.349:%3.19), avgs: 32 376: dt: 0.29, sse: 250.5 (0.051, 34.6, 0.000), neg: 27438 (%1.343:%3.19), avgs: 32 377: dt: 0.29, sse: 250.2 (0.051, 34.6, 0.000), neg: 27456 (%1.339:%3.18), avgs: 32 378: dt: 0.29, sse: 249.9 (0.051, 34.6, 0.000), neg: 27450 (%1.333:%3.17), avgs: 32 379: dt: 0.29, sse: 249.6 (0.051, 34.6, 0.000), neg: 27460 (%1.330:%3.16), avgs: 32 380: dt: 0.29, sse: 249.5 (0.051, 34.6, 0.000), neg: 27454 (%1.327:%3.15), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.32-->2.82) 381: dt: 0.29, sse: 249.4 (0.051, 34.6, 0.000), neg: 27446 (%1.325:%3.15), avgs: 32 382: dt: 0.29, sse: 249.2 (0.051, 34.6, 0.000), neg: 27444 (%1.322:%3.14), avgs: 32 383: dt: 0.29, sse: 249.0 (0.051, 34.6, 0.000), neg: 27438 (%1.319:%3.13), avgs: 32 384: dt: 0.29, sse: 248.9 (0.051, 34.6, 0.000), neg: 27421 (%1.317:%3.12), avgs: 32 385: dt: 0.29, sse: 248.7 (0.051, 34.6, 0.000), neg: 27418 (%1.313:%3.12), avgs: 32 386: dt: 155.64, sse: 241.3 (0.051, 34.3, 0.000), neg: 26865 (%1.190:%2.88), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.14) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.26-->2.81) 387: dt: 2.19, sse: 237.7 (0.051, 34.3, 0.000), neg: 26842 (%1.139:%2.86), avgs: 8 388: dt: 0.15, sse: 237.6 (0.051, 34.3, 0.000), neg: 26834 (%1.137:%2.87), avgs: 8 389: dt: 0.15, sse: 237.5 (0.051, 34.3, 0.000), neg: 26828 (%1.136:%2.87), avgs: 8 390: dt: 0.15, sse: 237.2 (0.051, 34.3, 0.000), neg: 26807 (%1.131:%2.86), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.18) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.27-->2.81) 391: dt: 0.15, sse: 236.9 (0.051, 34.3, 0.000), neg: 26807 (%1.126:%2.86), avgs: 8 392: dt: 0.15, sse: 236.5 (0.051, 34.3, 0.000), neg: 26810 (%1.121:%2.86), avgs: 8 393: dt: 0.15, sse: 236.2 (0.051, 34.3, 0.000), neg: 26798 (%1.116:%2.86), avgs: 8 394: dt: 0.15, sse: 235.8 (0.051, 34.3, 0.000), neg: 26789 (%1.110:%2.86), avgs: 8 395: dt: 0.15, sse: 235.5 (0.051, 34.3, 0.000), neg: 26775 (%1.105:%2.86), avgs: 8 396: dt: 0.15, sse: 235.2 (0.051, 34.3, 0.000), neg: 26753 (%1.100:%2.85), avgs: 8 397: dt: 0.15, sse: 234.8 (0.051, 34.3, 0.000), neg: 26743 (%1.094:%2.84), avgs: 8 398: dt: 15.35, sse: 232.1 (0.051, 34.2, 0.000), neg: 26547 (%1.053:%2.76), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.25-->2.82) 399: dt: 1.29, sse: 228.5 (0.051, 34.2, 0.000), neg: 26596 (%1.000:%2.76), avgs: 2 400: dt: 0.54, sse: 227.3 (0.051, 34.2, 0.000), neg: 26618 (%0.983:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.22-->2.82) 401: dt: 0.09, sse: 227.3 (0.051, 34.2, 0.000), neg: 26629 (%0.983:%2.75), avgs: 2 402: dt: 0.09, sse: 227.0 (0.051, 34.2, 0.000), neg: 26613 (%0.978:%2.75), avgs: 2 403: dt: 0.09, sse: 226.7 (0.051, 34.2, 0.000), neg: 26617 (%0.973:%2.76), avgs: 2 404: dt: 0.09, sse: 226.4 (0.051, 34.2, 0.000), neg: 26605 (%0.968:%2.76), avgs: 2 405: dt: 0.09, sse: 226.0 (0.051, 34.2, 0.000), neg: 26603 (%0.962:%2.76), avgs: 2 406: dt: 0.09, sse: 225.8 (0.051, 34.2, 0.000), neg: 26617 (%0.958:%2.77), avgs: 2 407: dt: 0.09, sse: 225.4 (0.051, 34.2, 0.000), neg: 26612 (%0.953:%2.77), avgs: 2 408: dt: 0.09, sse: 225.1 (0.051, 34.2, 0.000), neg: 26604 (%0.948:%2.77), avgs: 2 409: dt: 0.09, sse: 224.8 (0.051, 34.1, 0.000), neg: 26602 (%0.943:%2.76), avgs: 2 410: dt: 0.09, sse: 224.4 (0.051, 34.1, 0.000), neg: 26606 (%0.937:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.35) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 411: dt: 1.71, sse: 223.5 (0.051, 34.1, 0.000), neg: 26591 (%0.925:%2.71), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 412: dt: 0.03, sse: 223.1 (0.051, 34.1, 0.000), neg: 26666 (%0.918:%2.72), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
413: dt: 48.76, sse: 83.1 (0.051, 34.1, 0.000), neg: 26317 (%0.904:%2.68), avgs: 32 414: dt: 0.29, sse: 82.8 (0.051, 34.0, 0.000), neg: 26321 (%0.900:%2.68), avgs: 32 415: dt: 0.29, sse: 82.5 (0.051, 34.0, 0.000), neg: 26315 (%0.895:%2.68), avgs: 32 416: dt: 0.29, sse: 82.1 (0.051, 34.0, 0.000), neg: 26291 (%0.889:%2.67), avgs: 32 417: dt: 0.29, sse: 81.8 (0.051, 34.0, 0.000), neg: 26274 (%0.885:%2.67), avgs: 32 418: dt: 0.29, sse: 81.4 (0.051, 34.0, 0.000), neg: 26258 (%0.880:%2.66), avgs: 32 419: dt: 0.29, sse: 81.0 (0.051, 34.0, 0.000), neg: 26222 (%0.875:%2.65), avgs: 32 420: dt: 0.29, sse: 80.8 (0.051, 34.0, 0.000), neg: 26202 (%0.872:%2.64), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.29) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.84) 421: dt: 0.29, sse: 80.6 (0.051, 34.0, 0.000), neg: 26208 (%0.868:%2.64), avgs: 32 422: dt: 0.29, sse: 80.4 (0.051, 34.0, 0.000), neg: 26186 (%0.866:%2.64), avgs: 32 423: dt: 0.29, sse: 80.2 (0.051, 34.0, 0.000), neg: 26174 (%0.863:%2.64), avgs: 32 424: dt: 42.80, sse: 78.6 (0.051, 34.0, 0.000), neg: 26068 (%0.840:%2.60), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.84) 425: dt: 1.85, sse: 78.2 (0.051, 34.0, 0.000), neg: 26076 (%0.834:%2.57), avgs: 8 426: dt: 0.15, sse: 78.1 (0.051, 34.0, 0.000), neg: 26074 (%0.832:%2.57), avgs: 8 427: dt: 0.15, sse: 77.7 (0.051, 34.0, 0.000), neg: 26071 (%0.828:%2.57), avgs: 8 428: dt: 0.15, sse: 77.6 (0.051, 34.0, 0.000), neg: 26057 (%0.826:%2.57), avgs: 8 429: dt: 0.15, sse: 77.4 (0.051, 33.9, 0.000), neg: 26034 (%0.823:%2.57), avgs: 8 430: dt: 0.15, sse: 76.9 (0.051, 33.9, 0.000), neg: 26021 (%0.817:%2.56), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 431: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26008 (%0.814:%2.57), avgs: 8 432: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26015 (%0.814:%2.58), avgs: 8 433: dt: 0.15, sse: 76.5 (0.051, 33.9, 0.000), neg: 25996 (%0.811:%2.57), avgs: 8 434: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25991 (%0.808:%2.57), avgs: 8 435: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25997 (%0.808:%2.58), avgs: 8 436: dt: 1.20, sse: 76.2 (0.051, 33.9, 0.000), neg: 25992 (%0.805:%2.57), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 437: dt: 1.30, sse: 75.7 (0.051, 33.9, 0.000), neg: 26032 (%0.797:%2.57), avgs: 2 438: dt: 0.09, sse: 75.5 (0.051, 33.9, 0.000), neg: 26022 (%0.795:%2.57), avgs: 2 439: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26010 (%0.789:%2.56), avgs: 2 440: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26003 (%0.788:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.16) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.10-->2.85) 441: dt: 0.09, sse: 74.9 (0.051, 33.9, 0.000), neg: 26008 (%0.786:%2.57), avgs: 2 442: dt: 0.09, sse: 74.7 (0.051, 33.9, 0.000), neg: 26002 (%0.783:%2.57), avgs: 2 443: dt: 0.09, sse: 74.5 (0.051, 33.9, 0.000), neg: 26006 (%0.780:%2.58), avgs: 2 444: dt: 0.09, sse: 74.2 (0.051, 33.9, 0.000), neg: 26014 (%0.775:%2.58), avgs: 2 445: dt: 0.09, sse: 73.9 (0.051, 33.9, 0.000), neg: 26031 (%0.771:%2.58), avgs: 2 446: dt: 0.09, sse: 73.8 (0.051, 33.9, 0.000), neg: 26044 (%0.769:%2.59), avgs: 2 447: dt: 0.09, sse: 73.7 (0.051, 33.9, 0.000), neg: 26058 (%0.767:%2.61), avgs: 2 448: dt: 1.25, sse: 73.3 (0.051, 33.8, 0.000), neg: 25993 (%0.761:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.85) 449: dt: 0.03, sse: 73.2 (0.051, 33.8, 0.000), neg: 26076 (%0.760:%2.60), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.18-->2.85) 449: dt: 0.00, sse: 8423.5 (0.050, 33.8, 0.000), neg: 26076 (%0.754:%2.60), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours omentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.03/37 = 0.00088 epoch 3 (K=320.0), pass 1, starting sse = 256.64 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/38 = 0.00344 epoch 4 (K=1280.0), pass 1, starting sse = 83.95 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/37 = 0.00346 final distance error %100000.00 optimization complete. unfolding took 0.12 hours #-------------------------------------------- #@# Fix Topology lh Wed Mar 3 22:34:46 CET 2010
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/home/kutato/freesurfer/subjects/C1/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga C1 lh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters
Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ before topology correction, eno=-408 (nv=152952, nf=306720, ne=460080, g=205) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 56276 ambiguous faces found in tessellation segmenting defects... 92 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 4 -merging segment 0 into 5 -merging segment 29 into 27 -merging segment 32 into 30 -merging segment 71 into 49 -merging segment 4 into 52 -merging segment 74 into 72 85 defects to be corrected 0 vertices coincident reading input surface /home/kutato/freesurfer/subjects/C1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1015 (-4.5508) -vertex loglikelihood: -6.5092 (-3.2546) -normal dot loglikelihood: -3.5881 (-3.5881) -quad curv loglikelihood: -5.9652 (-2.9826) Total Loglikelihood : -25.1641
CORRECTING DEFECT 0 (vertices=48, convex hull=73) After retessellation of defect 0, euler #=-66 (121738,358994,237190) : difference with theory (-82) = -16
CORRECTING DEFECT 1 (vertices=172, convex hull=59) After retessellation of defect 1, euler #=-65 (121763,359092,237264) : difference with theory (-81) = -16
CORRECTING DEFECT 2 (vertices=14, convex hull=14) After retessellation of defect 2, euler #=-64 (121763,359095,237268) : difference with theory (-80) = -16
CORRECTING DEFECT 3 (vertices=4413, convex hull=721) After retessellation of defect 3, euler #=-67 (122638,362153,239448) : difference with theory (-79) = -12
CORRECTING DEFECT 4 (vertices=16, convex hull=21) After retessellation of defect 4, euler #=-66 (122639,362162,239457) : difference with theory (-78) = -12
CORRECTING DEFECT 5 (vertices=318, convex hull=123) After retessellation of defect 5, euler #=-65 (122682,362353,239606) : difference with theory (-77) = -12
CORRECTING DEFECT 6 (vertices=39, convex hull=81) After retessellation of defect 6, euler #=-64 (122698,362433,239671) : difference with theory (-76) = -12
CORRECTING DEFECT 7 (vertices=43, convex hull=30) After retessellation of defect 7, euler #=-63 (122702,362458,239693) : difference with theory (-75) = -12
CORRECTING DEFECT 8 (vertices=87, convex hull=103) After retessellation of defect 8, euler #=-62 (122736,362601,239803) : difference with theory (-74) = -12
CORRECTING DEFECT 9 (vertices=22, convex hull=52) After retessellation of defect 9, euler #=-61 (122744,362644,239839) : difference with theory (-73) = -12
CORRECTING DEFECT 10 (vertices=103, convex hull=78) After retessellation of defect 10, euler #=-60 (122768,362752,239924) : difference with theory (-72) = -12
CORRECTING DEFECT 11 (vertices=427, convex hull=253) After retessellation of defect 11, euler #=-59 (122927,363356,240370) : difference with theory (-71) = -12
CORRECTING DEFECT 12 (vertices=1508, convex hull=562) After retessellation of defect 12, euler #=-59 (123340,364897,241498) : difference with theory (-70) = -11
CORRECTING DEFECT 13 (vertices=57, convex hull=109) After retessellation of defect 13, euler #=-58 (123374,365043,241611) : difference with theory (-69) = -11
CORRECTING DEFECT 14 (vertices=49, convex hull=79) After retessellation of defect 14, euler #=-57 (123402,365159,241700) : difference with theory (-68) = -11
CORRECTING DEFECT 15 (vertices=69, convex hull=96) After retessellation of defect 15, euler #=-56 (123431,365288,241801) : difference with theory (-67) = -11
CORRECTING DEFECT 16 (vertices=29, convex hull=55) After retessellation of defect 16, euler #=-55 (123440,365339,241844) : difference with theory (-66) = -11
CORRECTING DEFECT 17 (vertices=14, convex hull=28) After retessellation of defect 17, euler #=-54 (123443,365354,241857) : difference with theory (-65) = -11
CORRECTING DEFECT 18 (vertices=41, convex hull=48) After retessellation of defect 18, euler #=-53 (123452,365398,241893) : difference with theory (-64) = -11
CORRECTING DEFECT 19 (vertices=459, convex hull=241) After retessellation of defect 19, euler #=-52 (123590,365935,242293) : difference with theory (-63) = -11
CORRECTING DEFECT 20 (vertices=55, convex hull=110) After retessellation of defect 20, euler #=-51 (123623,366080,242406) : difference with theory (-62) = -11
CORRECTING DEFECT 21 (vertices=478, convex hull=255) After retessellation of defect 21, euler #=-50 (123653,366319,242616) : difference with theory (-61) = -11
CORRECTING DEFECT 22 (vertices=27, convex hull=34) After retessellation of defect 22, euler #=-49 (123662,366357,242646) : difference with theory (-60) = -11
CORRECTING DEFECT 23 (vertices=53, convex hull=92) After retessellation of defect 23, euler #=-48 (123692,366487,242747) : difference with theory (-59) = -11
CORRECTING DEFECT 24 (vertices=32, convex hull=45) After retessellation of defect 24, euler #=-46 (123692,366504,242766) : difference with theory (-58) = -12
CORRECTING DEFECT 25 (vertices=181, convex hull=167) After retessellation of defect 25, euler #=-45 (123711,366644,242888) : difference with theory (-57) = -12
CORRECTING DEFECT 26 (vertices=1122, convex hull=340) After retessellation of defect 26, euler #=-45 (124058,367886,243783) : difference with theory (-56) = -11
CORRECTING DEFECT 27 (vertices=213, convex hull=67) After retessellation of defect 27, euler #=-44 (124080,367986,243862) : difference with theory (-55) = -11
CORRECTING DEFECT 28 (vertices=35, convex hull=22) After retessellation of defect 28, euler #=-43 (124085,368007,243879) : difference with theory (-54) = -11
CORRECTING DEFECT 29 (vertices=20, convex hull=63) After retessellation of defect 29, euler #=-42 (124095,368059,243922) : difference with theory (-53) = -11
CORRECTING DEFECT 30 (vertices=13, convex hull=26) After retessellation of defect 30, euler #=-41 (124096,368072,243935) : difference with theory (-52) = -11
CORRECTING DEFECT 31 (vertices=29, convex hull=74) After retessellation of defect 31, euler #=-40 (124105,368127,243982) : difference with theory (-51) = -11
CORRECTING DEFECT 32 (vertices=42, convex hull=33) After retessellation of defect 32, euler #=-39 (124109,368148,244000) : difference with theory (-50) = -11
CORRECTING DEFECT 33 (vertices=88, convex hull=93) After retessellation of defect 33, euler #=-38 (124124,368233,244071) : difference with theory (-49) = -11
CORRECTING DEFECT 34 (vertices=53, convex hull=67) After retessellation of defect 34, euler #=-37 (124137,368300,244126) : difference with theory (-48) = -11
CORRECTING DEFECT 35 (vertices=396, convex hull=152) After retessellation of defect 35, euler #=-36 (124283,368807,244488) : difference with theory (-47) = -11
CORRECTING DEFECT 36 (vertices=49, convex hull=71) After retessellation of defect 36, euler #=-35 (124310,368918,244573) : difference with theory (-46) = -11
CORRECTING DEFECT 37 (vertices=6, convex hull=20) After retessellation of defect 37, euler #=-34 (124311,368926,244581) : difference with theory (-45) = -11
CORRECTING DEFECT 38 (vertices=42, convex hull=81) After retessellation of defect 38, euler #=-33 (124337,369038,244668) : difference with theory (-44) = -11
CORRECTING DEFECT 39 (vertices=96, convex hull=66) After retessellation of defect 39, euler #=-32 (124378,369192,244782) : difference with theory (-43) = -11
CORRECTING DEFECT 40 (vertices=27, convex hull=34) After retessellation of defect 40, euler #=-31 (124382,369214,244801) : difference with theory (-42) = -11
CORRECTING DEFECT 41 (vertices=295, convex hull=174) After retessellation of defect 41, euler #=-30 (124455,369519,245034) : difference with theory (-41) = -11
CORRECTING DEFECT 42 (vertices=192, convex hull=126) After retessellation of defect 42, euler #=-29 (124483,369662,245150) : difference with theory (-40) = -11
CORRECTING DEFECT 43 (vertices=100, convex hull=110) After retessellation of defect 43, euler #=-28 (124549,369912,245335) : difference with theory (-39) = -11
CORRECTING DEFECT 44 (vertices=564, convex hull=398) After retessellation of defect 44, euler #=-27 (124766,370766,245973) : difference with theory (-38) = -11
CORRECTING DEFECT 45 (vertices=148, convex hull=121) After retessellation of defect 45, euler #=-26 (124843,371049,246180) : difference with theory (-37) = -11
CORRECTING DEFECT 46 (vertices=51, convex hull=75) After retessellation of defect 46, euler #=-25 (124855,371114,246234) : difference with theory (-36) = -11
CORRECTING DEFECT 47 (vertices=16122, convex hull=4397) normal vector of length zero at vertex 139578 with 0 faces vertex 139578 has 0 face Numerical result out of range Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 4 05:39:45 CET 2010
2010/3/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Gabor,
recon2-cp currently starts *after* the aseg, so you'll need to rerun it from an ealier point than that. Try using -autorecon2 instead.
cheers Bruce
On Wed, 3 Mar 2010, Perlaki Gabor wrote:
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
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Hi Bruce,
Then the problem is that we put the points in the cerebellum gray matter because we miss that part of cerebellum. Is there any method to correct the gray matter somehow?
Thanks a lot, Gabor
On Thu, 4 Mar 2010 09:01:48 -0500 (EST), Bruce Fischl wrote
hmmm, looks like there is a huge defect in the surface. Did you look at them to make sure nothing is very wrong (e.g. cerebellum attached to cortex)? Make sure you didn't include any control points in cerebellar gray matter, only in points that are in the interior of the white matter (and not for example in the dentate)
cheers, Bruce
On Thu, 4 Mar 2010, Gergely Orsi wrote:
Hi Bruce,
Thanks for your help. I've run the recon-all as you told (recon-all -autorecon2 -autorecon3 -subjid C1), but the recon-all exited with errors. I'm sending you the log. Could you help us some more?
Thank you.
Gergely Orsi
New invocation of recon-all
Wed Mar 3 16:00:17 CET 2010 /home/kutato/freesurfer/subjects/C1 /home/kutato/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid C1 subjid C1 setenv SUBJECTS_DIR /home/kutato/freesurfer/subjects FREESURFER_HOME /home/kutato/freesurfer Actual FREESURFER_HOME /home/kutato/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cachedMem: 4020216 2044228 1975988 0 182484 1237240 Swap: 8634360 0 8634360
######################################## program versions used $Id: recon-all,v 1.133.2.38 2009/01/08 19:49:55 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: tkregister2.c,v 1.86.2.7 2009/01/18 19:41:35 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_label.c,v 1.80.2.5 2008/08/15 21:00:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.5 2009/01/15 01:36:52 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature_stats.c,v 1.28.2.4 2008/10/02 21:42:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #------------------------------------- #@# EM Registration Wed Mar 3 16:00:18 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_em_register -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros)
spacing=8, using 2185 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 initial log_p = -84452.9
First Search limited to translation only.
Found translation: (-0.3, -12.2, -22.4): log p = -24312.3
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-24312.3 (thresh=-24288.0) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-12644.5 (thresh=-12631.8) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-12036.9, old_max_log_p =-12644.5 (thresh=-12631.8) 1.067 -0.009 -0.080 4.483; 0.020 1.198 0.188 -64.729; 0.090 -0.169 0.966 -5.663; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11905.9, old_max_log_p =-12036.9 (thresh=-12024.8) 1.050 -0.009 -0.079 6.394; 0.021 1.195 0.204 -66.521; 0.089 -0.185 0.948 -0.958; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11904.4, old_max_log_p =-11905.9 (thresh=-11894.0) 1.050 0.011 -0.076 3.377; 0.004 1.214 0.208 -67.391; 0.090 -0.188 0.963 -2.618; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11904.4 (thresh=-11892.5) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11516.2 (thresh=-11504.7) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 2185 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 11516.2 tol 0.000010 Resulting transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -11516.2 (old=-84452.9) transform before final EM align: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 244171 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1559944.8 tol 0.000000 final transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta... registration took 38 minutes and 54 seconds. #-------------------------------------- #@# CA Normalize Wed Mar 3 16:39:12 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
reading manually defined control points from /home/kutato/freesurfer/subjects/C1/tmp/control.dat using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 using 244171 sample points... INFO: compute sample coordinates transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 109.0 164 of 520 (31.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 112.0 208 of 519 (40.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 117.0 3 of 14 (21.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 121.0 4 of 21 (19.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 101.0 --> 116.0 6 of 51 (11.8%) samples deleted using 1125 total control points for intensity normalization... bias field = 1.011 +- 0.076 0 of 1450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 171 of 491 (34.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 113.0 132 of 559 (23.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 116.0 16 of 67 (23.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 117.0 10 of 70 (14.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 99.0 --> 113.0 12 of 94 (12.8%) samples deleted using 1281 total control points for intensity normalization... bias field = 0.994 +- 0.088 0 of 1650 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 210 of 555 (37.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 168 of 597 (28.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 113.0 21 of 79 (26.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 113.0 19 of 85 (22.4%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 91.0 --> 106.0 64 of 179 (35.8%) samples deleted using 1495 total control points for intensity normalization... bias field = 0.997 +- 0.082 0 of 1723 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Wed Mar 3 16:40:49 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.27 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.766, neg=0, invalid=766 0001: dt=228.525253, rms=0.731 (4.651%), neg=0, invalid=766 0002: dt=230.826667, rms=0.716 (1.976%), neg=0, invalid=766 0003: dt=131.235955, rms=0.711 (0.775%), neg=0, invalid=766 0004: dt=369.920000, rms=0.705 (0.719%), neg=0, invalid=766 0005: dt=134.901961, rms=0.702 (0.467%), neg=0, invalid=766 0006: dt=295.936000, rms=0.700 (0.338%), neg=0, invalid=766 0007: dt=129.472000, rms=0.698 (0.295%), neg=0, invalid=766 0008: dt=443.904000, rms=0.696 (0.269%), neg=0, invalid=766 0009: dt=142.933333, rms=0.694 (0.331%), neg=0, invalid=766 0010: dt=129.472000, rms=0.693 (0.073%), neg=0, invalid=766 0011: dt=129.472000, rms=0.692 (0.120%), neg=0, invalid=766 0012: dt=129.472000, rms=0.691 (0.183%), neg=0, invalid=766 0013: dt=129.472000, rms=0.689 (0.236%), neg=0, invalid=766 0014: dt=129.472000, rms=0.688 (0.265%), neg=0, invalid=766 0015: dt=129.472000, rms=0.686 (0.290%), neg=0, invalid=766 0016: dt=129.472000, rms=0.684 (0.282%), neg=0, invalid=766 0017: dt=129.472000, rms=0.682 (0.255%), neg=0, invalid=766 0018: dt=129.472000, rms=0.680 (0.239%), neg=0, invalid=766 0019: dt=129.472000, rms=0.679 (0.216%), neg=0, invalid=766 0020: dt=129.472000, rms=0.677 (0.204%), neg=0, invalid=766 0021: dt=129.472000, rms=0.676 (0.193%), neg=0, invalid=766 0022: dt=129.472000, rms=0.675 (0.166%), neg=0, invalid=766 0023: dt=129.472000, rms=0.674 (0.165%), neg=0, invalid=766 0024: dt=129.472000, rms=0.673 (0.171%), neg=0, invalid=766 0025: dt=129.472000, rms=0.672 (0.159%), neg=0, invalid=766 0026: dt=129.472000, rms=0.671 (0.137%), neg=0, invalid=766 0027: dt=129.472000, rms=0.670 (0.106%), neg=0, invalid=766 0028: dt=129.472000, rms=0.669 (0.111%), neg=0, invalid=766 0029: dt=129.472000, rms=0.668 (0.128%), neg=0, invalid=766 0030: dt=129.472000, rms=0.668 (0.109%), neg=0, invalid=766 0031: dt=129.472000, rms=0.667 (0.086%), neg=0, invalid=766 0032: dt=517.888000, rms=0.667 (0.023%), neg=0, invalid=766 0033: dt=517.888000, rms=0.667 (0.014%), neg=0, invalid=766 0034: dt=517.888000, rms=0.667 (-1.199%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0035: dt=129.472000, rms=0.665 (0.222%), neg=0, invalid=766 0036: dt=517.888000, rms=0.664 (0.233%), neg=0, invalid=766 0037: dt=129.472000, rms=0.664 (0.033%), neg=0, invalid=766 0038: dt=129.472000, rms=0.663 (0.026%), neg=0, invalid=766 0039: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0040: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0041: dt=129.472000, rms=0.662 (0.070%), neg=0, invalid=766 0042: dt=129.472000, rms=0.662 (0.085%), neg=0, invalid=766 0043: dt=129.472000, rms=0.661 (0.081%), neg=0, invalid=766 0044: dt=129.472000, rms=0.661 (0.066%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0045: dt=134.243902, rms=0.662 (0.847%), neg=0, invalid=766 0046: dt=136.900662, rms=0.651 (1.582%), neg=0, invalid=766 0047: dt=38.171429, rms=0.648 (0.467%), neg=0, invalid=766 0048: dt=145.152000, rms=0.645 (0.545%), neg=0, invalid=766 0049: dt=115.559395, rms=0.639 (0.880%), neg=0, invalid=766 0050: dt=36.288000, rms=0.638 (0.223%), neg=0, invalid=766 0051: dt=36.288000, rms=0.637 (0.131%), neg=0, invalid=766 0052: dt=36.288000, rms=0.635 (0.241%), neg=0, invalid=766 0053: dt=36.288000, rms=0.633 (0.377%), neg=0, invalid=766 0054: dt=36.288000, rms=0.630 (0.495%), neg=0, invalid=766 0055: dt=36.288000, rms=0.626 (0.531%), neg=0, invalid=766 0056: dt=36.288000, rms=0.623 (0.511%), neg=0, invalid=766 0057: dt=36.288000, rms=0.620 (0.485%), neg=0, invalid=766 0058: dt=36.288000, rms=0.617 (0.438%), neg=0, invalid=766 0059: dt=36.288000, rms=0.615 (0.421%), neg=0, invalid=766 0060: dt=36.288000, rms=0.612 (0.398%), neg=0, invalid=766 0061: dt=36.288000, rms=0.610 (0.353%), neg=0, invalid=766 0062: dt=36.288000, rms=0.609 (0.288%), neg=0, invalid=766 0063: dt=36.288000, rms=0.607 (0.241%), neg=0, invalid=766 0064: dt=36.288000, rms=0.606 (0.222%), neg=0, invalid=766 0065: dt=36.288000, rms=0.604 (0.208%), neg=0, invalid=766 0066: dt=36.288000, rms=0.603 (0.189%), neg=0, invalid=766 0067: dt=36.288000, rms=0.602 (0.167%), neg=0, invalid=766 0068: dt=36.288000, rms=0.601 (0.138%), neg=0, invalid=766 0069: dt=36.288000, rms=0.601 (0.134%), neg=0, invalid=766 0070: dt=36.288000, rms=0.600 (0.136%), neg=0, invalid=766 0071: dt=36.288000, rms=0.599 (0.142%), neg=0, invalid=766 0072: dt=36.288000, rms=0.598 (0.122%), neg=0, invalid=766 0073: dt=36.288000, rms=0.598 (0.110%), neg=0, invalid=766 0074: dt=124.416000, rms=0.597 (0.030%), neg=0, invalid=766 0075: dt=124.416000, rms=0.597 (-0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0076: dt=97.215190, rms=0.596 (0.268%), neg=0, invalid=766 0077: dt=37.647059, rms=0.595 (0.061%), neg=0, invalid=766 0078: dt=37.647059, rms=0.595 (0.033%), neg=0, invalid=766 0079: dt=37.647059, rms=0.595 (0.049%), neg=0, invalid=766 0080: dt=37.647059, rms=0.595 (0.050%), neg=0, invalid=766 0081: dt=37.647059, rms=0.594 (0.046%), neg=0, invalid=766 0082: dt=37.647059, rms=0.594 (0.028%), neg=0, invalid=766 0083: dt=36.288000, rms=0.594 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.59 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0084: dt=4.000000, rms=0.621 (0.022%), neg=0, invalid=766 0085: dt=1.600000, rms=0.621 (0.002%), neg=0, invalid=766 0086: dt=1.600000, rms=0.621 (0.001%), neg=0, invalid=766 0087: dt=1.600000, rms=0.621 (-0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0088: dt=1.600000, rms=0.621 (0.003%), neg=0, invalid=766 0089: dt=0.175000, rms=0.621 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0090: dt=5.778409, rms=0.671 (3.273%), neg=0, invalid=766 0091: dt=4.807692, rms=0.668 (0.356%), neg=0, invalid=766 0092: dt=2.304000, rms=0.668 (0.026%), neg=0, invalid=766 0093: dt=2.304000, rms=0.668 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 0094: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 0095: dt=0.384000, rms=0.717 (0.063%), neg=0, invalid=766 0096: dt=0.514706, rms=0.717 (0.077%), neg=0, invalid=766 0097: dt=1.280000, rms=0.716 (0.178%), neg=0, invalid=766 0098: dt=2.622951, rms=0.712 (0.483%), neg=0, invalid=766 0099: dt=0.448000, rms=0.712 (0.022%), neg=0, invalid=766 0100: dt=0.448000, rms=0.712 (0.029%), neg=0, invalid=766 0101: dt=0.448000, rms=0.711 (0.051%), neg=0, invalid=766 0102: dt=0.448000, rms=0.711 (0.065%), neg=0, invalid=766 0103: dt=0.448000, rms=0.711 (0.069%), neg=0, invalid=766 0104: dt=0.448000, rms=0.710 (0.049%), neg=0, invalid=766 0105: dt=0.448000, rms=0.710 (0.002%), neg=0, invalid=766 0106: dt=1.280000, rms=0.710 (0.013%), neg=0, invalid=766 0107: dt=3.307692, rms=0.709 (0.091%), neg=0, invalid=766 0108: dt=0.384000, rms=0.709 (0.016%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=766 0109: dt=1.024000, rms=0.709 (0.098%), neg=0, invalid=766 0110: dt=0.000000, rms=0.709 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=766 0111: dt=0.768240, rms=0.672 (2.434%), neg=0, invalid=766 0112: dt=0.028000, rms=0.671 (0.144%), neg=0, invalid=766 0113: dt=0.028000, rms=0.671 (-0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.671, neg=0, invalid=766 0114: dt=0.016000, rms=0.670 (0.020%), neg=0, invalid=766 0115: dt=0.000000, rms=0.670 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13848 (32) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, peak = 31), gca=30.6 gca peak = 0.14022 (22) mri peak = 0.14987 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, overlap=0.258) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, peak = 31), gca=31.3 gca peak = 0.24234 (100) mri peak = 0.17616 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.15860 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, overlap=0.633) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.09927 (79) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, peak = 77), gca=77.2 gca peak = 0.29892 (64) mri peak = 0.08177 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, overlap=0.005) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.06542 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.05686 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.02314 (77) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, peak = 80), gca=80.3 gca peak = 0.13270 (63) mri peak = 0.02476 (84) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, peak = 77), gca=77.2 gca peak = 0.15182 (70) mri peak = 0.16579 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, peak = 82), gca=82.2 gca peak = 0.14251 (76) mri peak = 0.22639 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, overlap=0.339) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.02272 (74) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, peak = 80), gca=79.5 gca peak = 0.12723 (61) mri peak = 0.02272 (77) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, peak = 82), gca=82.3 gca peak = 0.22684 (88) mri peak = 0.06491 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, peak = 112), gca=112.2 gca peak = 0.21067 (87) mri peak = 0.06839 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, peak = 109), gca=108.8 gca peak = 0.25455 (62) mri peak = 0.16005 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, peak = 78), gca=77.5 gca peak = 0.39668 (62) mri peak = 0.19364 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.08041 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, overlap=0.801) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.08539 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, overlap=0.548) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, peak = 98), gca=97.9 gca peak = 0.13716 (82) mri peak = 0.09766 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, overlap=0.375) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, peak = 92), gca=92.2 gca peak = 0.15214 (84) mri peak = 0.10719 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, overlap=0.371) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.08349 (101) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, overlap=0.001) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, peak = 102), gca=102.0 gca peak = 0.11809 (92) mri peak = 0.09947 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07866 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.19514 (33) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, overlap=0.860) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, peak = 32), gca=32.4 gca peak = 0.13542 (27) mri peak = 0.12763 (32) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, peak = 34), gca=34.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.22 x + 0.0 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... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0116: dt=108.542373, rms=0.671 (3.115%), neg=0, invalid=766 0117: dt=247.972125, rms=0.664 (1.098%), neg=0, invalid=766 0118: dt=192.927536, rms=0.659 (0.715%), neg=0, invalid=766 0119: dt=87.482014, rms=0.657 (0.292%), neg=0, invalid=766 0120: dt=517.888000, rms=0.653 (0.661%), neg=0, invalid=766 0121: dt=77.748148, rms=0.651 (0.220%), neg=0, invalid=766 0122: dt=2071.552000, rms=0.643 (1.306%), neg=0, invalid=766 0123: dt=71.896869, rms=0.640 (0.383%), neg=0, invalid=766 0124: dt=129.472000, rms=0.640 (0.109%), neg=0, invalid=766 0125: dt=517.888000, rms=0.637 (0.376%), neg=0, invalid=766 0126: dt=73.984000, rms=0.637 (0.062%), neg=0, invalid=766 0127: dt=887.808000, rms=0.635 (0.288%), neg=0, invalid=766 0128: dt=129.472000, rms=0.634 (0.235%), neg=0, invalid=766 0129: dt=517.888000, rms=0.633 (0.150%), neg=0, invalid=766 0130: dt=129.472000, rms=0.632 (0.119%), neg=0, invalid=766 0131: dt=295.936000, rms=0.631 (0.082%), neg=0, invalid=766 0132: dt=129.472000, rms=0.631 (0.085%), neg=0, invalid=766 0133: dt=221.952000, rms=0.630 (0.065%), neg=0, invalid=766 0134: dt=129.472000, rms=0.630 (0.073%), neg=0, invalid=766 0135: dt=295.936000, rms=0.630 (0.058%), neg=0, invalid=766 0136: dt=129.472000, rms=0.629 (0.094%), neg=0, invalid=766 0137: dt=110.976000, rms=0.629 (0.022%), neg=0, invalid=766 0138: dt=110.976000, rms=0.629 (0.053%), neg=0, invalid=766 0139: dt=110.976000, rms=0.628 (0.073%), neg=0, invalid=766 0140: dt=110.976000, rms=0.628 (0.081%), neg=0, invalid=766 0141: dt=110.976000, rms=0.627 (0.103%), neg=0, invalid=766 0142: dt=110.976000, rms=0.626 (0.149%), neg=0, invalid=766 0143: dt=110.976000, rms=0.625 (0.151%), neg=0, invalid=766 0144: dt=110.976000, rms=0.624 (0.152%), neg=0, invalid=766 0145: dt=110.976000, rms=0.623 (0.156%), neg=0, invalid=766 0146: dt=110.976000, rms=0.622 (0.160%), neg=0, invalid=766 0147: dt=110.976000, rms=0.621 (0.164%), neg=0, invalid=766 0148: dt=110.976000, rms=0.620 (0.157%), neg=0, invalid=766 0149: dt=110.976000, rms=0.619 (0.155%), neg=0, invalid=766 0150: dt=110.976000, rms=0.618 (0.154%), neg=0, invalid=766 0151: dt=110.976000, rms=0.617 (0.144%), neg=0, invalid=766 0152: dt=110.976000, rms=0.617 (0.122%), neg=0, invalid=766 0153: dt=110.976000, rms=0.616 (0.134%), neg=0, invalid=766 0154: dt=110.976000, rms=0.615 (0.147%), neg=0, invalid=766 0155: dt=110.976000, rms=0.614 (0.136%), neg=0, invalid=766 0156: dt=110.976000, rms=0.613 (0.119%), neg=0, invalid=766 0157: dt=110.976000, rms=0.613 (0.094%), neg=0, invalid=766 0158: dt=110.976000, rms=0.612 (0.112%), neg=0, invalid=766 0159: dt=110.976000, rms=0.611 (0.119%), neg=0, invalid=766 0160: dt=110.976000, rms=0.611 (0.098%), neg=0, invalid=766 0161: dt=110.976000, rms=0.610 (0.070%), neg=0, invalid=766 0162: dt=110.976000, rms=0.610 (0.093%), neg=0, invalid=766 0163: dt=110.976000, rms=0.609 (0.101%), neg=0, invalid=766 0164: dt=110.976000, rms=0.609 (0.086%), neg=0, invalid=766 0165: dt=110.976000, rms=0.608 (0.069%), neg=0, invalid=766 0166: dt=110.976000, rms=0.608 (0.081%), neg=0, invalid=766 0167: dt=110.976000, rms=0.607 (0.080%), neg=0, invalid=766 0168: dt=110.976000, rms=0.607 (0.067%), neg=0, invalid=766 0169: dt=110.976000, rms=0.606 (0.054%), neg=0, invalid=766 0170: dt=110.976000, rms=0.606 (0.060%), neg=0, invalid=766 0171: dt=110.976000, rms=0.606 (0.064%), neg=0, invalid=766 0172: dt=110.976000, rms=0.605 (0.066%), neg=0, invalid=766 0173: dt=110.976000, rms=0.605 (0.054%), neg=0, invalid=766 0174: dt=110.976000, rms=0.605 (0.053%), neg=0, invalid=766 0175: dt=110.976000, rms=0.604 (0.052%), neg=0, invalid=766 0176: dt=110.976000, rms=0.604 (0.048%), neg=0, invalid=766 0177: dt=110.976000, rms=0.604 (0.045%), neg=0, invalid=766 0178: dt=110.976000, rms=0.604 (0.043%), neg=0, invalid=766 0179: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=766 0180: dt=110.976000, rms=0.603 (0.050%), neg=0, invalid=766 0181: dt=110.976000, rms=0.603 (0.047%), neg=0, invalid=766 0182: dt=110.976000, rms=0.602 (0.035%), neg=0, invalid=766 0183: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=766 0184: dt=110.976000, rms=0.602 (0.040%), neg=0, invalid=766 0185: dt=110.976000, rms=0.602 (0.037%), neg=0, invalid=766 0186: dt=110.976000, rms=0.602 (0.033%), neg=0, invalid=766 0187: dt=110.976000, rms=0.601 (0.037%), neg=0, invalid=766 0188: dt=110.976000, rms=0.601 (0.030%), neg=0, invalid=766 0189: dt=110.976000, rms=0.601 (0.035%), neg=0, invalid=766 0190: dt=110.976000, rms=0.601 (0.040%), neg=0, invalid=766 0191: dt=110.976000, rms=0.601 (0.031%), neg=0, invalid=766 0192: dt=110.976000, rms=0.600 (0.027%), neg=0, invalid=766 0193: dt=110.976000, rms=0.600 (0.038%), neg=0, invalid=766 0194: dt=110.976000, rms=0.600 (0.035%), neg=0, invalid=766 0195: dt=110.976000, rms=0.600 (0.023%), neg=0, invalid=766 0196: dt=110.976000, rms=0.600 (0.028%), neg=0, invalid=766 0197: dt=110.976000, rms=0.599 (0.032%), neg=0, invalid=766 0198: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0199: dt=110.976000, rms=0.599 (0.027%), neg=0, invalid=766 0200: dt=110.976000, rms=0.599 (0.026%), neg=0, invalid=766 0201: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0202: dt=110.976000, rms=0.599 (0.028%), neg=0, invalid=766 0203: dt=110.976000, rms=0.598 (0.022%), neg=0, invalid=766 0204: dt=110.976000, rms=0.598 (0.032%), neg=0, invalid=766 0205: dt=110.976000, rms=0.598 (0.028%), neg=0, invalid=766 0206: dt=110.976000, rms=0.598 (0.021%), neg=0, invalid=766 0207: dt=110.976000, rms=0.598 (0.023%), neg=0, invalid=766 0208: dt=110.976000, rms=0.598 (0.024%), neg=0, invalid=766 0209: dt=110.976000, rms=0.598 (0.025%), neg=0, invalid=766 0210: dt=110.976000, rms=0.597 (0.020%), neg=0, invalid=766 0211: dt=221.952000, rms=0.597 (0.001%), neg=0, invalid=766 0212: dt=221.952000, rms=0.597 (0.014%), neg=0, invalid=766 0213: dt=221.952000, rms=0.597 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0214: dt=221.952000, rms=0.597 (0.077%), neg=0, invalid=766 0215: dt=443.904000, rms=0.596 (0.152%), neg=0, invalid=766 0216: dt=32.368000, rms=0.596 (0.018%), neg=0, invalid=766 0217: dt=32.368000, rms=0.596 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 0218: dt=112.375587, rms=0.596 (0.426%), neg=0, invalid=766 0219: dt=67.729134, rms=0.592 (0.773%), neg=0, invalid=766 0220: dt=31.104000, rms=0.590 (0.211%), neg=0, invalid=766 0221: dt=580.608000, rms=0.577 (2.307%), neg=0, invalid=766 0222: dt=64.000000, rms=0.574 (0.535%), neg=0, invalid=766 0223: dt=25.920000, rms=0.573 (0.091%), neg=0, invalid=766 0224: dt=331.776000, rms=0.571 (0.410%), neg=0, invalid=766 0225: dt=50.070588, rms=0.568 (0.559%), neg=0, invalid=766 0226: dt=20.736000, rms=0.567 (0.042%), neg=0, invalid=766 0227: dt=20.736000, rms=0.567 (0.035%), neg=0, invalid=766 0228: dt=20.736000, rms=0.567 (0.064%), neg=0, invalid=766 0229: dt=20.736000, rms=0.566 (0.111%), neg=0, invalid=766 0230: dt=20.736000, rms=0.565 (0.159%), neg=0, invalid=766 0231: dt=20.736000, rms=0.564 (0.176%), neg=0, invalid=766 0232: dt=20.736000, rms=0.563 (0.180%), neg=0, invalid=766 0233: dt=20.736000, rms=0.562 (0.180%), neg=0, invalid=766 0234: dt=20.736000, rms=0.561 (0.186%), neg=0, invalid=766 0235: dt=20.736000, rms=0.560 (0.201%), neg=0, invalid=766 0236: dt=20.736000, rms=0.559 (0.226%), neg=0, invalid=766 0237: dt=20.736000, rms=0.558 (0.230%), neg=0, invalid=766 0238: dt=20.736000, rms=0.556 (0.228%), neg=0, invalid=766 0239: dt=20.736000, rms=0.555 (0.216%), neg=0, invalid=766 0240: dt=20.736000, rms=0.554 (0.199%), neg=0, invalid=766 0241: dt=20.736000, rms=0.553 (0.192%), neg=0, invalid=766 0242: dt=20.736000, rms=0.552 (0.199%), neg=0, invalid=766 0243: dt=20.736000, rms=0.551 (0.198%), neg=0, invalid=766 0244: dt=20.736000, rms=0.550 (0.186%), neg=0, invalid=766 0245: dt=20.736000, rms=0.549 (0.175%), neg=0, invalid=766 0246: dt=20.736000, rms=0.548 (0.168%), neg=0, invalid=766 0247: dt=20.736000, rms=0.547 (0.160%), neg=0, invalid=766 0248: dt=20.736000, rms=0.546 (0.158%), neg=0, invalid=766 0249: dt=20.736000, rms=0.545 (0.159%), neg=0, invalid=766 0250: dt=20.736000, rms=0.544 (0.150%), neg=0, invalid=766 0251: dt=20.736000, rms=0.544 (0.138%), neg=0, invalid=766 0252: dt=20.736000, rms=0.543 (0.131%), neg=0, invalid=766 0253: dt=20.736000, rms=0.542 (0.127%), neg=0, invalid=766 0254: dt=20.736000, rms=0.542 (0.119%), neg=0, invalid=766 0255: dt=20.736000, rms=0.541 (0.117%), neg=0, invalid=766 0256: dt=20.736000, rms=0.540 (0.117%), neg=0, invalid=766 0257: dt=20.736000, rms=0.540 (0.109%), neg=0, invalid=766 0258: dt=20.736000, rms=0.539 (0.104%), neg=0, invalid=766 0259: dt=20.736000, rms=0.539 (0.098%), neg=0, invalid=766 0260: dt=20.736000, rms=0.538 (0.095%), neg=0, invalid=766 0261: dt=20.736000, rms=0.538 (0.093%), neg=0, invalid=766 0262: dt=20.736000, rms=0.537 (0.087%), neg=0, invalid=766 0263: dt=20.736000, rms=0.537 (0.081%), neg=0, invalid=766 0264: dt=20.736000, rms=0.536 (0.076%), neg=0, invalid=766 0265: dt=20.736000, rms=0.536 (0.075%), neg=0, invalid=766 0266: dt=20.736000, rms=0.535 (0.074%), neg=0, invalid=766 0267: dt=20.736000, rms=0.535 (0.073%), neg=0, invalid=766 0268: dt=20.736000, rms=0.535 (0.071%), neg=0, invalid=766 0269: dt=20.736000, rms=0.534 (0.067%), neg=0, invalid=766 0270: dt=20.736000, rms=0.534 (0.068%), neg=0, invalid=766 0271: dt=20.736000, rms=0.534 (0.066%), neg=0, invalid=766 0272: dt=20.736000, rms=0.533 (0.063%), neg=0, invalid=766 0273: dt=20.736000, rms=0.533 (0.058%), neg=0, invalid=766 0274: dt=20.736000, rms=0.533 (0.062%), neg=0, invalid=766 0275: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0276: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0277: dt=20.736000, rms=0.532 (0.059%), neg=0, invalid=766 0278: dt=20.736000, rms=0.531 (0.054%), neg=0, invalid=766 0279: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0280: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0281: dt=20.736000, rms=0.531 (0.045%), neg=0, invalid=766 0282: dt=20.736000, rms=0.530 (0.047%), neg=0, invalid=766 0283: dt=20.736000, rms=0.530 (0.050%), neg=0, invalid=766 0284: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0285: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0286: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0287: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0288: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0289: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0290: dt=20.736000, rms=0.529 (0.037%), neg=0, invalid=766 0291: dt=20.736000, rms=0.528 (0.037%), neg=0, invalid=766 0292: dt=20.736000, rms=0.528 (0.033%), neg=0, invalid=766 0293: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0294: dt=20.736000, rms=0.528 (0.035%), neg=0, invalid=766 0295: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0296: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0297: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0298: dt=20.736000, rms=0.527 (0.030%), neg=0, invalid=766 0299: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0300: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0301: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0302: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0303: dt=20.736000, rms=0.526 (0.031%), neg=0, invalid=766 0304: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0305: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0306: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0307: dt=20.736000, rms=0.526 (0.024%), neg=0, invalid=766 0308: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0309: dt=20.736000, rms=0.526 (0.027%), neg=0, invalid=766 0310: dt=20.736000, rms=0.526 (0.023%), neg=0, invalid=766 0311: dt=20.736000, rms=0.525 (0.026%), neg=0, invalid=766 0312: dt=20.736000, rms=0.525 (0.022%), neg=0, invalid=766 0313: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0314: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0315: dt=580.608000, rms=0.525 (0.040%), neg=0, invalid=766 0316: dt=31.104000, rms=0.525 (0.015%), neg=0, invalid=766 0317: dt=31.104000, rms=0.525 (0.007%), neg=0, invalid=766 0318: dt=31.104000, rms=0.525 (0.004%), neg=0, invalid=766 0319: dt=31.104000, rms=0.525 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=766 0320: dt=136.072072, rms=0.523 (0.371%), neg=0, invalid=766 0321: dt=36.288000, rms=0.522 (0.046%), neg=0, invalid=766 0322: dt=36.288000, rms=0.522 (0.054%), neg=0, invalid=766 0323: dt=36.288000, rms=0.522 (0.039%), neg=0, invalid=766 0324: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=766 0325: dt=36.288000, rms=0.522 (0.058%), neg=0, invalid=766 0326: dt=36.288000, rms=0.521 (0.085%), neg=0, invalid=766 0327: dt=36.288000, rms=0.521 (0.066%), neg=0, invalid=766 0328: dt=36.288000, rms=0.521 (0.044%), neg=0, invalid=766 0329: dt=36.288000, rms=0.520 (0.041%), neg=0, invalid=766 0330: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0331: dt=36.288000, rms=0.520 (0.046%), neg=0, invalid=766 0332: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0333: dt=36.288000, rms=0.519 (0.056%), neg=0, invalid=766 0334: dt=36.288000, rms=0.519 (0.055%), neg=0, invalid=766 0335: dt=36.288000, rms=0.519 (0.053%), neg=0, invalid=766 0336: dt=36.288000, rms=0.518 (0.052%), neg=0, invalid=766 0337: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0338: dt=36.288000, rms=0.518 (0.042%), neg=0, invalid=766 0339: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0340: dt=36.288000, rms=0.518 (0.047%), neg=0, invalid=766 0341: dt=36.288000, rms=0.517 (0.046%), neg=0, invalid=766 0342: dt=36.288000, rms=0.517 (0.035%), neg=0, invalid=766 0343: dt=36.288000, rms=0.517 (0.036%), neg=0, invalid=766 0344: dt=36.288000, rms=0.517 (0.033%), neg=0, invalid=766 0345: dt=36.288000, rms=0.517 (0.031%), neg=0, invalid=766 0346: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0347: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0348: dt=36.288000, rms=0.516 (0.038%), neg=0, invalid=766 0349: dt=36.288000, rms=0.516 (0.033%), neg=0, invalid=766 0350: dt=36.288000, rms=0.516 (0.034%), neg=0, invalid=766 0351: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0352: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0353: dt=36.288000, rms=0.515 (0.027%), neg=0, invalid=766 0354: dt=36.288000, rms=0.515 (0.032%), neg=0, invalid=766 0355: dt=36.288000, rms=0.515 (0.036%), neg=0, invalid=766 0356: dt=36.288000, rms=0.515 (0.031%), neg=0, invalid=766 0357: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0358: dt=36.288000, rms=0.515 (0.022%), neg=0, invalid=766 0359: dt=36.288000, rms=0.514 (0.028%), neg=0, invalid=766 0360: dt=36.288000, rms=0.514 (0.026%), neg=0, invalid=766 0361: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0362: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0363: dt=36.288000, rms=0.514 (0.024%), neg=0, invalid=766 0364: dt=124.416000, rms=0.514 (0.012%), neg=0, invalid=766 0365: dt=124.416000, rms=0.514 (-0.159%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 0366: dt=20.227979, rms=0.525 (0.130%), neg=0, invalid=766 0367: dt=31.326316, rms=0.524 (0.190%), neg=0, invalid=766 0368: dt=12.972973, rms=0.523 (0.137%), neg=0, invalid=766 0369: dt=59.508772, rms=0.522 (0.302%), neg=0, invalid=766 0370: dt=13.479452, rms=0.521 (0.263%), neg=0, invalid=766 0371: dt=179.200000, rms=0.517 (0.721%), neg=0, invalid=766 0372: dt=24.457539, rms=0.514 (0.537%), neg=0, invalid=766 0373: dt=21.157025, rms=0.513 (0.170%), neg=0, invalid=766 0374: dt=38.303030, rms=0.512 (0.170%), neg=0, invalid=766 0375: dt=11.200000, rms=0.512 (0.098%), neg=0, invalid=766 0376: dt=44.800000, rms=0.511 (0.160%), neg=0, invalid=766 0377: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=766 0378: dt=38.400000, rms=0.510 (0.132%), neg=0, invalid=766 0379: dt=11.200000, rms=0.509 (0.068%), neg=0, invalid=766 0380: dt=25.600000, rms=0.509 (0.079%), neg=0, invalid=766 0381: dt=11.200000, rms=0.509 (0.048%), neg=0, invalid=766 0382: dt=11.200000, rms=0.509 (0.055%), neg=0, invalid=766 0383: dt=11.200000, rms=0.508 (0.066%), neg=0, invalid=766 0384: dt=11.200000, rms=0.508 (0.092%), neg=0, invalid=766 0385: dt=11.200000, rms=0.507 (0.109%), neg=0, invalid=766 0386: dt=11.200000, rms=0.506 (0.139%), neg=0, invalid=766 0387: dt=11.200000, rms=0.506 (0.146%), neg=0, invalid=766 0388: dt=11.200000, rms=0.505 (0.155%), neg=0, invalid=766 0389: dt=11.200000, rms=0.504 (0.151%), neg=0, invalid=766 0390: dt=11.200000, rms=0.503 (0.168%), neg=0, invalid=766 0391: dt=11.200000, rms=0.503 (0.165%), neg=0, invalid=766 0392: dt=11.200000, rms=0.502 (0.158%), neg=0, invalid=766 0393: dt=11.200000, rms=0.501 (0.146%), neg=0, invalid=766 0394: dt=11.200000, rms=0.500 (0.133%), neg=0, invalid=766 0395: dt=11.200000, rms=0.500 (0.140%), neg=0, invalid=766 0396: dt=11.200000, rms=0.499 (0.132%), neg=0, invalid=766 0397: dt=11.200000, rms=0.498 (0.118%), neg=0, invalid=766 0398: dt=11.200000, rms=0.498 (0.112%), neg=0, invalid=766 0399: dt=11.200000, rms=0.497 (0.116%), neg=0, invalid=766 0400: dt=11.200000, rms=0.497 (0.105%), neg=0, invalid=766 0401: dt=11.200000, rms=0.496 (0.097%), neg=0, invalid=766 0402: dt=11.200000, rms=0.496 (0.083%), neg=0, invalid=766 0403: dt=11.200000, rms=0.495 (0.089%), neg=0, invalid=766 0404: dt=11.200000, rms=0.495 (0.084%), neg=0, invalid=766 0405: dt=11.200000, rms=0.495 (0.074%), neg=0, invalid=766 0406: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0407: dt=11.200000, rms=0.494 (0.060%), neg=0, invalid=766 0408: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0409: dt=11.200000, rms=0.493 (0.054%), neg=0, invalid=766 0410: dt=11.200000, rms=0.493 (0.053%), neg=0, invalid=766 0411: dt=11.200000, rms=0.493 (0.040%), neg=0, invalid=766 0412: dt=11.200000, rms=0.493 (0.051%), neg=0, invalid=766 0413: dt=11.200000, rms=0.493 (0.041%), neg=0, invalid=766 0414: dt=11.200000, rms=0.492 (0.040%), neg=0, invalid=766 0415: dt=11.200000, rms=0.492 (0.035%), neg=0, invalid=766 0416: dt=11.200000, rms=0.492 (0.041%), neg=0, invalid=766 0417: dt=11.200000, rms=0.492 (0.045%), neg=0, invalid=766 0418: dt=11.200000, rms=0.492 (0.031%), neg=0, invalid=766 0419: dt=11.200000, rms=0.491 (0.026%), neg=0, invalid=766 0420: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0421: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0422: dt=11.200000, rms=0.491 (0.023%), neg=0, invalid=766 0423: dt=11.200000, rms=0.491 (0.019%), neg=0, invalid=766 0424: dt=25.600000, rms=0.491 (0.018%), neg=0, invalid=766 0425: dt=25.600000, rms=0.491 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=766 0426: dt=28.444444, rms=0.490 (0.167%), neg=0, invalid=766 0427: dt=12.000000, rms=0.490 (0.084%), neg=0, invalid=766 0428: dt=9.600000, rms=0.489 (0.017%), neg=0, invalid=766 0429: dt=9.600000, rms=0.489 (0.022%), neg=0, invalid=766 0430: dt=9.600000, rms=0.489 (0.014%), neg=0, invalid=766 0431: dt=9.600000, rms=0.489 (0.005%), neg=0, invalid=766 0432: dt=25.600000, rms=0.489 (0.013%), neg=0, invalid=766 0433: dt=4.000000, rms=0.489 (0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0434: dt=0.000000, rms=0.519 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0435: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=766 0436: dt=1.963333, rms=0.567 (1.560%), neg=0, invalid=766 0437: dt=0.525000, rms=0.567 (0.074%), neg=0, invalid=766 0438: dt=0.448000, rms=0.567 (0.019%), neg=0, invalid=766 0439: dt=0.448000, rms=0.567 (-0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=766 0440: dt=1.282051, rms=0.566 (0.177%), neg=0, invalid=766 0441: dt=0.448000, rms=0.565 (0.014%), neg=0, invalid=766 0442: dt=0.448000, rms=0.565 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 0443: dt=0.448000, rms=0.502 (2.666%), neg=0, invalid=766 0444: dt=0.448000, rms=0.499 (0.609%), neg=0, invalid=766 0445: dt=0.448000, rms=0.497 (0.408%), neg=0, invalid=766 0446: dt=0.448000, rms=0.495 (0.275%), neg=0, invalid=766 0447: dt=0.448000, rms=0.494 (0.209%), neg=0, invalid=766 0448: dt=0.448000, rms=0.493 (0.162%), neg=0, invalid=766 0449: dt=0.028000, rms=0.493 (0.007%), neg=0, invalid=766 0450: dt=0.028000, rms=0.493 (0.009%), neg=0, invalid=766 0451: dt=0.028000, rms=0.493 (0.015%), neg=0, invalid=766 0452: dt=0.028000, rms=0.493 (0.023%), neg=0, invalid=766 0453: dt=0.028000, rms=0.493 (0.028%), neg=0, invalid=766 0454: dt=0.028000, rms=0.493 (0.031%), neg=0, invalid=766 0455: dt=0.028000, rms=0.493 (0.037%), neg=0, invalid=766 0456: dt=0.028000, rms=0.492 (0.038%), neg=0, invalid=766 0457: dt=0.028000, rms=0.492 (0.039%), neg=0, invalid=766 0458: dt=0.028000, rms=0.492 (0.043%), neg=0, invalid=766 0459: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0460: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0461: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0462: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0463: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0464: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0465: dt=0.028000, rms=0.491 (0.039%), neg=0, invalid=766 0466: dt=0.028000, rms=0.490 (0.039%), neg=0, invalid=766 0467: dt=0.028000, rms=0.490 (0.036%), neg=0, invalid=766 0468: dt=0.028000, rms=0.490 (0.002%), neg=0, invalid=766 0469: dt=0.028000, rms=0.490 (0.004%), neg=0, invalid=766 0470: dt=0.028000, rms=0.490 (0.006%), neg=0, invalid=766 0471: dt=0.028000, rms=0.490 (0.008%), neg=0, invalid=766 0472: dt=0.028000, rms=0.490 (0.007%), neg=0, invalid=766 0473: dt=0.461538, rms=0.490 (0.033%), neg=0, invalid=766 0474: dt=0.024000, rms=0.490 (0.001%), neg=0, invalid=766 0475: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0476: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0477: dt=0.024000, rms=0.490 (0.004%), neg=0, invalid=766 0478: dt=0.024000, rms=0.490 (0.005%), neg=0, invalid=766 0479: dt=0.024000, rms=0.490 (0.006%), neg=0, invalid=766 0480: dt=0.024000, rms=0.490 (0.007%), neg=0, invalid=766 0481: dt=0.024000, rms=0.490 (0.008%), neg=0, invalid=766 0482: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0483: dt=0.024000, rms=0.490 (0.009%), neg=0, invalid=766 0484: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0485: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0486: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0487: dt=0.024000, rms=0.489 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=766 0488: dt=0.384000, rms=0.486 (0.728%), neg=0, invalid=766 0489: dt=0.028000, rms=0.486 (0.009%), neg=0, invalid=766 0490: dt=0.028000, rms=0.486 (0.010%), neg=0, invalid=766 0491: dt=0.028000, rms=0.486 (0.017%), neg=0, invalid=766 0492: dt=0.028000, rms=0.486 (0.024%), neg=0, invalid=766 0493: dt=0.028000, rms=0.485 (0.027%), neg=0, invalid=766 0494: dt=0.028000, rms=0.485 (0.030%), neg=0, invalid=766 0495: dt=0.028000, rms=0.485 (0.029%), neg=0, invalid=766 0496: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=766 0497: dt=0.028000, rms=0.485 (0.026%), neg=0, invalid=766 0498: dt=0.028000, rms=0.485 (0.024%), neg=0, invalid=766 0499: dt=0.028000, rms=0.485 (0.018%), neg=0, invalid=766 0500: dt=0.000000, rms=0.485 (-0.001%), neg=0, invalid=766 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... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 0501: dt=73.984000, rms=0.483 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=766 0502: dt=129.472000, rms=0.482 (0.113%), neg=0, invalid=766 0503: dt=221.952000, rms=0.482 (0.068%), neg=0, invalid=766 0504: dt=129.472000, rms=0.481 (0.056%), neg=0, invalid=766 0505: dt=110.976000, rms=0.481 (0.027%), neg=0, invalid=766 0506: dt=110.976000, rms=0.481 (0.030%), neg=0, invalid=766 0507: dt=110.976000, rms=0.481 (0.041%), neg=0, invalid=766 0508: dt=110.976000, rms=0.481 (0.053%), neg=0, invalid=766 0509: dt=110.976000, rms=0.481 (0.049%), neg=0, invalid=766 0510: dt=110.976000, rms=0.480 (0.059%), neg=0, invalid=766 0511: dt=110.976000, rms=0.480 (0.053%), neg=0, invalid=766 0512: dt=110.976000, rms=0.480 (0.054%), neg=0, invalid=766 0513: dt=110.976000, rms=0.480 (0.049%), neg=0, invalid=766 0514: dt=110.976000, rms=0.479 (0.049%), neg=0, invalid=766 0515: dt=110.976000, rms=0.479 (0.047%), neg=0, invalid=766 0516: dt=110.976000, rms=0.479 (0.044%), neg=0, invalid=766 0517: dt=110.976000, rms=0.479 (0.043%), neg=0, invalid=766 0518: dt=110.976000, rms=0.478 (0.037%), neg=0, invalid=766 0519: dt=110.976000, rms=0.478 (0.036%), neg=0, invalid=766 0520: dt=110.976000, rms=0.478 (0.031%), neg=0, invalid=766 0521: dt=110.976000, rms=0.478 (0.030%), neg=0, invalid=766 0522: dt=110.976000, rms=0.478 (0.028%), neg=0, invalid=766 0523: dt=110.976000, rms=0.478 (0.025%), neg=0, invalid=766 0524: dt=110.976000, rms=0.478 (0.022%), neg=0, invalid=766 0525: dt=443.904000, rms=0.478 (0.005%), neg=0, invalid=766 0526: dt=443.904000, rms=0.478 (-0.062%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 0527: dt=38.588235, rms=0.477 (0.078%), neg=0, invalid=766 0528: dt=103.680000, rms=0.477 (0.118%), neg=0, invalid=766 0529: dt=145.152000, rms=0.475 (0.331%), neg=0, invalid=766 0530: dt=36.288000, rms=0.475 (0.018%), neg=0, invalid=766 0531: dt=36.288000, rms=0.475 (0.035%), neg=0, invalid=766 0532: dt=36.288000, rms=0.475 (0.064%), neg=0, invalid=766 0533: dt=36.288000, rms=0.474 (0.087%), neg=0, invalid=766 0534: dt=36.288000, rms=0.474 (0.100%), neg=0, invalid=766 0535: dt=18.144000, rms=0.474 (0.019%), neg=0, invalid=766 0536: dt=9.072000, rms=0.474 (0.010%), neg=0, invalid=766 0537: dt=6.480000, rms=0.474 (0.007%), neg=0, invalid=766 0538: dt=0.101250, rms=0.474 (0.000%), neg=0, invalid=766 0539: dt=0.025312, rms=0.474 (0.000%), neg=0, invalid=766 0540: dt=0.012656, rms=0.474 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 0541: dt=132.512821, rms=0.471 (0.546%), neg=0, invalid=766 0542: dt=44.800000, rms=0.470 (0.141%), neg=0, invalid=766 0543: dt=103.680000, rms=0.470 (0.116%), neg=0, invalid=766 0544: dt=414.720000, rms=0.468 (0.287%), neg=0, invalid=766 0545: dt=43.000000, rms=0.468 (0.096%), neg=0, invalid=766 0546: dt=36.288000, rms=0.468 (0.019%), neg=0, invalid=766 0547: dt=36.288000, rms=0.468 (0.017%), neg=0, invalid=766 0548: dt=18.144000, rms=0.468 (0.008%), neg=0, invalid=766 0549: dt=9.072000, rms=0.468 (0.004%), neg=0, invalid=766 0550: dt=9.072000, rms=0.468 (0.005%), neg=0, invalid=766 0551: dt=0.567000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 0552: dt=11.200000, rms=0.467 (0.281%), neg=0, invalid=766 0553: dt=0.700000, rms=0.467 (0.016%), neg=0, invalid=766 0554: dt=0.350000, rms=0.467 (0.008%), neg=0, invalid=766 0555: dt=0.175000, rms=0.467 (0.004%), neg=0, invalid=766 0556: dt=0.021875, rms=0.467 (0.000%), neg=0, invalid=766 0557: dt=0.000684, rms=0.467 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0558: dt=44.800000, rms=0.462 (1.098%), neg=0, invalid=766 0559: dt=44.800000, rms=0.459 (0.606%), neg=0, invalid=766 0560: dt=38.400000, rms=0.457 (0.489%), neg=0, invalid=766 0561: dt=44.800000, rms=0.456 (0.222%), neg=0, invalid=766 0562: dt=11.200000, rms=0.455 (0.147%), neg=0, invalid=766 0563: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0564: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0565: dt=0.043750, rms=0.455 (0.000%), neg=0, invalid=766 0566: dt=0.005469, rms=0.455 (0.000%), neg=0, invalid=766 0567: dt=0.000684, rms=0.455 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0568: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0569: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 0570: dt=0.906250, rms=0.465 (0.232%), neg=0, invalid=766 0571: dt=0.448000, rms=0.464 (0.065%), neg=0, invalid=766 0572: dt=0.681818, rms=0.464 (0.070%), neg=0, invalid=766 0573: dt=1.792000, rms=0.464 (0.057%), neg=0, invalid=766 0574: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 0575: dt=0.100000, rms=0.464 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0576: dt=1.536000, rms=0.463 (0.243%), neg=0, invalid=766 0577: dt=0.541667, rms=0.462 (0.043%), neg=0, invalid=766 0578: dt=0.541667, rms=0.462 (0.036%), neg=0, invalid=766 0579: dt=0.541667, rms=0.462 (0.056%), neg=0, invalid=766 0580: dt=0.541667, rms=0.462 (0.018%), neg=0, invalid=766 0581: dt=0.541667, rms=0.462 (0.027%), neg=0, invalid=766 0582: dt=0.541667, rms=0.462 (0.024%), neg=0, invalid=766 0583: dt=0.541667, rms=0.462 (0.010%), neg=0, invalid=766 0584: dt=0.000000, rms=0.462 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 0585: dt=0.140550, rms=0.451 (0.763%), neg=0, invalid=766 0586: dt=0.122596, rms=0.449 (0.477%), neg=0, invalid=766 0587: dt=0.112257, rms=0.448 (0.334%), neg=0, invalid=766 0588: dt=0.112000, rms=0.447 (0.265%), neg=0, invalid=766 0589: dt=0.112000, rms=0.446 (0.214%), neg=0, invalid=766 0590: dt=0.112000, rms=0.445 (0.174%), neg=0, invalid=766 0591: dt=0.112000, rms=0.444 (0.144%), neg=0, invalid=766 0592: dt=0.112000, rms=0.444 (0.120%), neg=0, invalid=766 0593: dt=0.112000, rms=0.443 (0.101%), neg=0, invalid=766 0594: dt=0.112000, rms=0.443 (0.086%), neg=0, invalid=766 0595: dt=0.112000, rms=0.442 (0.074%), neg=0, invalid=766 0596: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0597: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0598: dt=0.028000, rms=0.442 (0.029%), neg=0, invalid=766 0599: dt=0.028000, rms=0.442 (0.040%), neg=0, invalid=766 0600: dt=0.028000, rms=0.442 (0.049%), neg=0, invalid=766 0601: dt=0.028000, rms=0.442 (0.011%), neg=0, invalid=766 0602: dt=0.028000, rms=0.442 (0.021%), neg=0, invalid=766 0603: dt=0.028000, rms=0.442 (0.030%), neg=0, invalid=766 0604: dt=0.028000, rms=0.441 (0.037%), neg=0, invalid=766 0605: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0606: dt=0.028000, rms=0.441 (0.045%), neg=0, invalid=766 0607: dt=0.028000, rms=0.441 (0.007%), neg=0, invalid=766 0608: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0609: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0610: dt=0.112000, rms=0.441 (0.025%), neg=0, invalid=766 0611: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0612: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0613: dt=0.028000, rms=0.441 (0.011%), neg=0, invalid=766 0614: dt=0.028000, rms=0.441 (0.015%), neg=0, invalid=766 0615: dt=0.028000, rms=0.441 (0.018%), neg=0, invalid=766 0616: dt=0.028000, rms=0.440 (0.021%), neg=0, invalid=766 0617: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 0618: dt=0.028000, rms=0.440 (0.008%), neg=0, invalid=766 0619: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=766 0620: dt=0.028000, rms=0.440 (0.058%), neg=0, invalid=766 0621: dt=0.028000, rms=0.440 (0.054%), neg=0, invalid=766 0622: dt=0.024000, rms=0.440 (0.043%), neg=0, invalid=766 0623: dt=0.024000, rms=0.439 (0.041%), neg=0, invalid=766 0624: dt=0.024000, rms=0.439 (0.075%), neg=0, invalid=766 0625: dt=0.024000, rms=0.439 (0.035%), neg=0, invalid=766 0626: dt=0.024000, rms=0.439 (0.064%), neg=0, invalid=766 0627: dt=0.024000, rms=0.438 (0.086%), neg=0, invalid=766 0628: dt=0.024000, rms=0.438 (0.101%), neg=0, invalid=766 0629: dt=0.024000, rms=0.437 (0.108%), neg=0, invalid=766 0630: dt=0.024000, rms=0.437 (0.109%), neg=0, invalid=766 0631: dt=0.024000, rms=0.436 (0.104%), neg=0, invalid=766 0632: dt=0.024000, rms=0.436 (0.095%), neg=0, invalid=766 0633: dt=0.024000, rms=0.436 (0.082%), neg=0, invalid=766 0634: dt=0.024000, rms=0.435 (0.068%), neg=0, invalid=766 0635: dt=0.024000, rms=0.435 (0.053%), neg=0, invalid=766 0636: dt=0.024000, rms=0.435 (0.038%), neg=0, invalid=766 0637: dt=0.024000, rms=0.435 (0.023%), neg=0, invalid=766 0638: dt=0.024000, rms=0.435 (0.009%), neg=0, invalid=766 0639: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 4 hours, 9 minutes and 13 seconds. #-------------------------------------- #@# CA Reg Inv Wed Mar 3 20:50:02 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Mar 3 20:51:02 CET 2010
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11104963 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA Wed Mar 3 20:52:16 CET 2010
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.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 '/home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (45, 52, 28) --> (207, 202, 237) using (99, 102, 133) as brain centroid... mean wm in atlas = 126, using box (79,84,107) --> (118, 120,158) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 140, scaling input intensities by 0.900 scaling channel 0 by 0.9
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-17103.0 (thresh=-17085.9) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-14667.9 (thresh=-14653.3) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14488.4, old_max_log_p =-14667.9 (thresh=-14653.3) 1.036 -0.063 -0.081 14.725; 0.070 1.213 0.222 -79.106; 0.083 -0.208 0.964 -0.991; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14488.4 (thresh=-14473.9) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14436.8 (thresh=-14422.4) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14436.8 (thresh=-14422.4) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14336.6 (thresh=-14322.3) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 3481 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 14336.6 tol 0.000010 Resulting transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -14336.6 (old=-17103.0) transform before final EM align: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 382743 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1833208.1 tol 0.000000 final transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta... registration took 49 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Wed Mar 3 21:42:15 CET 2010
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
$Id: mri_seg_diff.c,v 1.3.2.1 2008/09/03 22:02:00 nicks Exp $ cwd /home/kutato/freesurfer/subjects/C1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname localhost.localdomain machine x86_64 user kutato Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmenations No difference found.
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /home/kutato/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /home/kutato/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, overlap=0.688) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, peak = 32), gca=32.4 gca peak = 0.14982 (20) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, overlap=0.231) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, peak = 28), gca=28.5 gca peak = 0.28003 (97) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, peak = 102), gca=101.8 gca peak = 0.18160 (96) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, overlap=0.407) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, peak = 78), gca=77.5 gca peak = 0.32745 (63) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, peak = 77), gca=77.2 gca peak = 0.08597 (105) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, overlap=0.045) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, peak = 80), gca=80.3 gca peak = 0.08598 (64) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, overlap=0.074) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, peak = 85), gca=85.2 gca peak = 0.18227 (75) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, overlap=0.228) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, peak = 84), gca=84.4 gca peak = 0.10629 (62) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, peak = 85), gca=85.2 gca peak = 0.11668 (59) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, peak = 83), gca=82.6 gca peak = 0.17849 (88) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, peak = 112), gca=112.2 gca peak = 0.16819 (86) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, peak = 108), gca=107.5 gca peak = 0.41688 (64) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, peak = 80), gca=80.0 gca peak = 0.42394 (62) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, peak = 81), gca=80.6 gca peak = 0.10041 (96) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, overlap=0.774) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, overlap=0.443) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, overlap=0.331) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, peak = 91), gca=91.1 gca peak = 0.09624 (82) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, overlap=0.394) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, overlap=0.000) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, peak = 103), gca=103.4 gca peak = 0.12757 (95) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, overlap=0.525) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, overlap=0.902) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, peak = 32), gca=32.4 gca peak = 0.26069 (23) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, overlap=0.240) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.23 x + 0.0 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14396 (33) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, overlap=0.871) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, peak = 31), gca=31.4 gca peak = 0.13467 (29) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, overlap=0.673) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, peak = 31), gca=31.2 gca peak = 0.27948 (102) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, peak = 102), gca=102.0 gca peak = 0.18507 (101) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, peak = 101), gca=101.0 gca peak = 0.21463 (78) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, peak = 76), gca=76.1 gca peak = 0.27122 (77) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 77), gca=77.0 gca peak = 0.08007 (112) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, overlap=0.810) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, peak = 112), gca=112.0 gca peak = 0.08789 (111) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, overlap=0.795) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, peak = 114), gca=113.8 gca peak = 0.06240 (80) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, overlap=0.591) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, peak = 78), gca=78.0 gca peak = 0.07094 (77) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, overlap=0.711) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, peak = 75), gca=75.1 gca peak = 0.23769 (85) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, peak = 85), gca=85.0 gca peak = 0.13104 (84) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, overlap=0.845) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, peak = 86), gca=86.1 gca peak = 0.08141 (85) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, overlap=0.690) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, peak = 83), gca=82.9 gca peak = 0.09212 (83) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, overlap=0.736) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, peak = 83), gca=83.0 gca peak = 0.14004 (112) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, overlap=0.965) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, peak = 112), gca=112.0 gca peak = 0.13912 (108) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, peak = 108), gca=108.0 gca peak = 0.30905 (79) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 81), gca=81.0 gca peak = 0.37870 (81) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, peak = 79), gca=79.0 gca peak = 0.10116 (99) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, overlap=0.963) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, peak = 99), gca=99.0 gca peak = 0.09774 (97) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, overlap=0.918) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, peak = 97), gca=97.0 gca peak = 0.08941 (98) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, peak = 98), gca=98.0 gca peak = 0.08263 (85) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, overlap=0.828) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, peak = 85), gca=85.0 gca peak = 0.06255 (104) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, overlap=0.638) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, peak = 104), gca=104.0 gca peak = 0.14189 (104) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, overlap=0.808) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, peak = 104), gca=104.0 gca peak = 0.16147 (99) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, peak = 99), gca=99.0 gca peak = 0.22647 (34) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, overlap=0.851) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, peak = 33), gca=33.2 gca peak = 0.16050 (32) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, overlap=0.781) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, peak = 32), gca=32.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26758 (43) gca peak CSF = 0.17739 (47) gca peak Left_Accumbens_area = 0.36131 (79) gca peak Left_undetermined = 0.95107 (38) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.22906 (40) gca peak Right_Accumbens_area = 0.27742 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.12959 (48) gca peak Fifth_Ventricle = 0.50102 (51) gca peak WM_hypointensities = 0.15008 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34132 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 33062 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 306 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77084 changed. image ll: -2.213, PF=1.000 pass 2: 12120 changed. image ll: -2.211, PF=1.000 pass 3: 4101 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 30 minutes and 38 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz C1
reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /home/kutato/freesurfer/subjects/C1/mri/aseg.auto_noCCseg.mgz reading norm from /home/kutato/freesurfer/subjects/C1/mri/norm.mgz 44494 voxels in left wm, 85128 in right wm, xrange [115, 131] global minimum found at slice 125.0, rotations (-3.75, -0.25) final transformation (x=125.0, yr=-3.750, zr=-0.250): 0.998 0.004 -0.065 11.082; -0.004 1.000 0.000 0.509; 0.065 0.000 0.998 -7.901; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 133 113 eigenvectors: -0.002 -0.003 1.000; -0.035 -0.999 -0.003; 0.999 -0.035 0.002; error in mid anterior detected - correcting... writing aseg with callosum to to /home/kutato/freesurfer/subjects/C1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.8 minutes #-------------------------------------- #@# Merge ASeg Wed Mar 3 22:14:45 CET 2010
cp aseg.auto.mgz aseg.mgz
#-------------------------------------------- #@# Intensity Normalization2 Wed Mar 3 22:14:45 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using control points from file /home/kutato/freesurfer/subjects/C1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 710 control points... only using 710 control points from file... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 223389 control points removed building Voronoi diagram... performing soap bubble smoothing... 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 brain.mgz 3D bias adjustment took 6 minutes and 6 seconds. using MR volume brainmask.mgz to mask input volume... using wm (255) threshold 245.0 for removing exterior voxels white matter peak found at 111 gm peak at 77 (77), valley at 40 (40) csf peak at 28, setting threshold to 60 white matter peak found at 111 gm peak at 78 (78), valley at 40 (40) csf peak at 29, setting threshold to 61 #-------------------------------------------- #@# Mask BFS Wed Mar 3 22:20:55 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Mar 3 22:20:58 CET 2010
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (109.0): 107.5 +- 7.5 [80.0 --> 125.0] GM (68.0) : 65.0 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10488 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4151 filled 110391 bright non-wm voxels segmented. 7168 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz...
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume... auto filling took 0.76 minutes reading wm segmentation from wm.seg.mgz... 404 voxels added to wm to prevent paths from MTL structures to cortex 6112 additional wm voxels added 0 additional wm voxels added SEG EDIT: 68648 voxels turned on, 46182 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 90 new 90 115,126,128 old 90 new 90 writing edited volume to wm.asegedit.mgz....
mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1 pass 1 (xy+): 154 found - 154 modified | TOTAL: 154 pass 2 (xy+): 0 found - 154 modified | TOTAL: 154 pass 1 (xy-): 134 found - 134 modified | TOTAL: 288 pass 2 (xy-): 0 found - 134 modified | TOTAL: 288 pass 1 (yz+): 124 found - 124 modified | TOTAL: 412 pass 2 (yz+): 0 found - 124 modified | TOTAL: 412 pass 1 (yz-): 99 found - 99 modified | TOTAL: 511 pass 2 (yz-): 0 found - 99 modified | TOTAL: 511 pass 1 (xz+): 137 found - 137 modified | TOTAL: 648 pass 2 (xz+): 0 found - 137 modified | TOTAL: 648 pass 1 (xz-): 124 found - 124 modified | TOTAL: 772 pass 2 (xz-): 0 found - 124 modified | TOTAL: 772 Iteration Number : 1 pass 1 (+++): 100 found - 100 modified | TOTAL: 100 pass 2 (+++): 0 found - 100 modified | TOTAL: 100 pass 1 (+++): 97 found - 97 modified | TOTAL: 197 pass 2 (+++): 0 found - 97 modified | TOTAL: 197 pass 1 (+++): 84 found - 84 modified | TOTAL: 281 pass 2 (+++): 0 found - 84 modified | TOTAL: 281 pass 1 (+++): 135 found - 135 modified | TOTAL: 416 pass 2 (+++): 0 found - 135 modified | TOTAL: 416 Iteration Number : 1 pass 1 (++): 141 found - 141 modified | TOTAL: 141 pass 2 (++): 0 found - 141 modified | TOTAL: 141 pass 1 (+-): 205 found - 205 modified | TOTAL: 346 pass 2 (+-): 0 found - 205 modified | TOTAL: 346 pass 1 (--): 152 found - 152 modified | TOTAL: 498 pass 2 (--): 1 found - 153 modified | TOTAL: 499 pass 3 (--): 0 found - 153 modified | TOTAL: 499 pass 1 (-+): 183 found - 183 modified | TOTAL: 682 pass 2 (-+): 0 found - 183 modified | TOTAL: 682 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 23 found - 23 modified | TOTAL: 45 pass 2 (xy-): 0 found - 23 modified | TOTAL: 45 pass 1 (yz+): 19 found - 19 modified | TOTAL: 64 pass 2 (yz+): 0 found - 19 modified | TOTAL: 64 pass 1 (yz-): 37 found - 37 modified | TOTAL: 101 pass 2 (yz-): 0 found - 37 modified | TOTAL: 101 pass 1 (xz+): 39 found - 39 modified | TOTAL: 140 pass 2 (xz+): 0 found - 39 modified | TOTAL: 140 pass 1 (xz-): 22 found - 22 modified | TOTAL: 162 pass 2 (xz-): 0 found - 22 modified | TOTAL: 162 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 pass 1 (+++): 4 found - 4 modified | TOTAL: 19 pass 2 (+++): 0 found - 4 modified | TOTAL: 19 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 22 found - 22 modified | TOTAL: 35 pass 2 (+-): 0 found - 22 modified | TOTAL: 35 pass 1 (--): 17 found - 17 modified | TOTAL: 52 pass 2 (--): 0 found - 17 modified | TOTAL: 52 pass 1 (-+): 10 found - 10 modified | TOTAL: 62 pass 2 (-+): 0 found - 10 modified | TOTAL: 62 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 2131 (out of 674704: 0.315842) keeping edits binarizing input wm segmentation... Ambiguous edge configurations...
Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels
mri_pretess done
#-------------------------------------------- #@# Fill Wed Mar 3 22:23:31 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 619 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 119, 151), TAL = (2.0, 23.0, 9.0) talairach voxel to voxel transform 0.943 0.014 0.050 -0.471; -0.002 0.809 -0.158 52.074; -0.063 0.140 0.999 12.198; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 119, 151) --> (2.0, 23.0, 9.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 23.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 9.00) SRC: (110.64, 124.32, 172.81) search lh wm seed point around talairach space (-16.00, 23.00, 9.00), SRC: (144.61, 124.24, 170.53) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Mar 3 22:24:28 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 12 found - 12 modified | TOTAL: 25 pass 2 (xy-): 0 found - 12 modified | TOTAL: 25 pass 1 (yz+): 10 found - 10 modified | TOTAL: 35 pass 2 (yz+): 0 found - 10 modified | TOTAL: 35 pass 1 (yz-): 22 found - 22 modified | TOTAL: 57 pass 2 (yz-): 0 found - 22 modified | TOTAL: 57 pass 1 (xz+): 15 found - 15 modified | TOTAL: 72 pass 2 (xz+): 0 found - 15 modified | TOTAL: 72 pass 1 (xz-): 5 found - 5 modified | TOTAL: 77 pass 2 (xz-): 0 found - 5 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 9 found - 9 modified | TOTAL: 15 pass 2 (+-): 0 found - 9 modified | TOTAL: 15 pass 1 (--): 13 found - 13 modified | TOTAL: 28 pass 2 (--): 0 found - 13 modified | TOTAL: 28 pass 1 (-+): 3 found - 3 modified | TOTAL: 31 pass 2 (-+): 0 found - 3 modified | TOTAL: 31 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 128 (out of 320366: 0.039954) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ slice 50: 715 vertices, 806 faces slice 60: 6587 vertices, 6870 faces slice 70: 16362 vertices, 16829 faces slice 80: 27996 vertices, 28461 faces slice 90: 40299 vertices, 40842 faces slice 100: 52688 vertices, 53229 faces slice 110: 65001 vertices, 65581 faces slice 120: 77662 vertices, 78249 faces slice 130: 89134 vertices, 89714 faces slice 140: 100712 vertices, 101362 faces slice 150: 112906 vertices, 113608 faces slice 160: 123188 vertices, 123863 faces slice 170: 130916 vertices, 131557 faces slice 180: 137022 vertices, 137584 faces slice 190: 141777 vertices, 142325 faces slice 200: 145789 vertices, 146310 faces slice 210: 149464 vertices, 149996 faces slice 220: 152836 vertices, 153278 faces slice 230: 152952 vertices, 153360 faces slice 240: 152952 vertices, 153360 faces slice 250: 152952 vertices, 153360 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components... 152952 voxel in cpt #1: X=-408 [v=152952,e=460080,f=306720] located at (-25.554226, -6.675813, -2.117488) For the whole surface: X=-408 [v=152952,e=460080,f=306720] One single component has been found nothing to do done
#-------------------------------------------- #@# Smooth1 lh Wed Mar 3 22:24:41 CET 2010
mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/kutato/freesurfer/subjects/C1/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Mar 3 22:24:46 CET 2010
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/kutato/freesurfer/subjects/C1/scripts avg radius = 49.0 mm, total surface area = 79501 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.071 (target=0.015) step 030: RMS=0.069 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.065 (target=0.015) step 045: RMS=0.065 (target=0.015) step 050: RMS=0.065 (target=0.015) step 055: RMS=0.065 (target=0.015) step 060: RMS=0.065 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Mar 3 22:25:42 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, sigma=0.0, host=local, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90
surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.88 (0.00-->27.18) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-1.82-->2.32) tol=1.0e-01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
301: dt: 15.53, sse: 8540.7 (0.052, 34.9, 0.000), neg: 26636 (%4.389:%4.53), avgs: 32 302: dt: 0.29, sse: 8539.7 (0.052, 34.9, 0.000), neg: 26636 (%4.375:%4.52), avgs: 32 303: dt: 0.29, sse: 8538.0 (0.052, 34.9, 0.000), neg: 26627 (%4.349:%4.52), avgs: 32 304: dt: 0.29, sse: 8536.1 (0.052, 34.9, 0.000), neg: 26615 (%4.318:%4.51), avgs: 32 305: dt: 0.29, sse: 8533.4 (0.052, 34.9, 0.000), neg: 26609 (%4.275:%4.50), avgs: 32 306: dt: 0.29, sse: 8530.6 (0.052, 34.8, 0.000), neg: 26596 (%4.228:%4.49), avgs: 32 307: dt: 0.29, sse: 8527.6 (0.052, 34.8, 0.000), neg: 26579 (%4.176:%4.48), avgs: 32 308: dt: 0.29, sse: 8524.4 (0.052, 34.8, 0.000), neg: 26560 (%4.119:%4.46), avgs: 32 309: dt: 0.29, sse: 8520.9 (0.052, 34.8, 0.000), neg: 26543 (%4.058:%4.45), avgs: 32 310: dt: 0.29, sse: 8517.4 (0.051, 34.8, 0.000), neg: 26523 (%3.994:%4.43), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->25.82) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.93-->2.40) 311: dt: 0.29, sse: 8514.0 (0.051, 34.8, 0.000), neg: 26509 (%3.932:%4.41), avgs: 32 312: dt: 48.14, sse: 8479.7 (0.051, 34.6, 0.000), neg: 26094 (%3.212:%4.03), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->24.45) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.71-->2.54) 313: dt: 3.56, sse: 8469.9 (0.051, 34.7, 0.000), neg: 26269 (%2.998:%4.03), avgs: 8 314: dt: 0.15, sse: 8469.3 (0.051, 34.7, 0.000), neg: 26242 (%2.986:%4.01), avgs: 8 315: dt: 0.15, sse: 8468.6 (0.051, 34.7, 0.000), neg: 26253 (%2.969:%4.00), avgs: 8 316: dt: 0.15, sse: 8467.1 (0.051, 34.7, 0.000), neg: 26267 (%2.942:%3.99), avgs: 8 317: dt: 0.15, sse: 8466.2 (0.051, 34.7, 0.000), neg: 26292 (%2.922:%3.98), avgs: 8 318: dt: 0.15, sse: 8465.3 (0.051, 34.7, 0.000), neg: 26295 (%2.901:%3.97), avgs: 8 319: dt: 0.15, sse: 8465.2 (0.051, 34.7, 0.000), neg: 26300 (%2.890:%3.96), avgs: 8 320: dt: 0.15, sse: 8464.7 (0.051, 34.7, 0.000), neg: 26310 (%2.872:%3.95), avgs: 8 vertex spacing 0.98 +- 0.88 (0.00-->23.63) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.52-->2.61) 321: dt: 0.15, sse: 8464.2 (0.051, 34.7, 0.000), neg: 26327 (%2.854:%3.94), avgs: 8 322: dt: 0.15, sse: 8463.7 (0.051, 34.7, 0.000), neg: 26343 (%2.835:%3.93), avgs: 8 323: dt: 0.15, sse: 8462.9 (0.051, 34.7, 0.000), neg: 26359 (%2.810:%3.93), avgs: 8 324: dt: 2.69, sse: 8458.0 (0.051, 34.7, 0.000), neg: 26415 (%2.703:%3.92), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->23.23) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.47-->2.64) 325: dt: 1.44, sse: 8454.2 (0.051, 34.7, 0.000), neg: 26661 (%2.601:%3.93), avgs: 2 326: dt: 0.09, sse: 8453.8 (0.051, 34.7, 0.000), neg: 26697 (%2.581:%3.93), avgs: 2 327: dt: 0.09, sse: 8452.8 (0.051, 34.8, 0.000), neg: 26737 (%2.553:%3.93), avgs: 2 328: dt: 0.09, sse: 8451.9 (0.051, 34.8, 0.000), neg: 26779 (%2.526:%3.92), avgs: 2 329: dt: 0.09, sse: 8451.5 (0.051, 34.8, 0.000), neg: 26818 (%2.503:%3.92), avgs: 2 330: dt: 0.09, sse: 8450.9 (0.051, 34.8, 0.000), neg: 26880 (%2.480:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.65) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.26-->2.69) 331: dt: 0.09, sse: 8450.2 (0.051, 34.8, 0.000), neg: 26944 (%2.455:%3.91), avgs: 2 332: dt: 0.09, sse: 8449.5 (0.051, 34.8, 0.000), neg: 27007 (%2.430:%3.92), avgs: 2 333: dt: 0.09, sse: 8449.1 (0.051, 34.8, 0.000), neg: 27074 (%2.410:%3.91), avgs: 2 334: dt: 0.09, sse: 8448.9 (0.051, 34.9, 0.000), neg: 27156 (%2.391:%3.92), avgs: 2 335: dt: 0.09, sse: 8448.2 (0.051, 34.9, 0.000), neg: 27231 (%2.368:%3.92), avgs: 2 336: dt: 0.06, sse: 8448.1 (0.051, 34.9, 0.000), neg: 27244 (%2.366:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.33) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.39-->2.72) 337: dt: 0.16, sse: 8447.2 (0.051, 34.9, 0.000), neg: 27436 (%2.337:%3.96), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.21-->2.72) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
338: dt: 107.53, sse: 1470.7 (0.051, 34.6, 0.000), neg: 26824 (%1.951:%3.54), avgs: 32 scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.782, avgs=0 005/300: dt: 0.9000, rms radial error=177.523, avgs=0 010/300: dt: 0.9000, rms radial error=176.967, avgs=0 015/300: dt: 0.9000, rms radial error=176.237, avgs=0 020/300: dt: 0.9000, rms radial error=175.406, avgs=0 025/300: dt: 0.9000, rms radial error=174.516, avgs=0 030/300: dt: 0.9000, rms radial error=173.592, avgs=0 035/300: dt: 0.9000, rms radial error=172.654, avgs=0 040/300: dt: 0.9000, rms radial error=171.710, avgs=0 045/300: dt: 0.9000, rms radial error=170.765, avgs=0 050/300: dt: 0.9000, rms radial error=169.821, avgs=0 055/300: dt: 0.9000, rms radial error=168.881, avgs=0 060/300: dt: 0.9000, rms radial error=167.944, avgs=0 065/300: dt: 0.9000, rms radial error=167.011, avgs=0 070/300: dt: 0.9000, rms radial error=166.083, avgs=0 075/300: dt: 0.9000, rms radial error=165.160, avgs=0 080/300: dt: 0.9000, rms radial error=164.243, avgs=0 085/300: dt: 0.9000, rms radial error=163.332, avgs=0 090/300: dt: 0.9000, rms radial error=162.426, avgs=0 095/300: dt: 0.9000, rms radial error=161.525, avgs=0 100/300: dt: 0.9000, rms radial error=160.628, avgs=0 105/300: dt: 0.9000, rms radial error=159.737, avgs=0 110/300: dt: 0.9000, rms radial error=158.850, avgs=0 115/300: dt: 0.9000, rms radial error=157.968, avgs=0 120/300: dt: 0.9000, rms radial error=157.091, avgs=0 125/300: dt: 0.9000, rms radial error=156.218, avgs=0 130/300: dt: 0.9000, rms radial error=155.350, avgs=0 135/300: dt: 0.9000, rms radial error=154.488, avgs=0 140/300: dt: 0.9000, rms radial error=153.631, avgs=0 145/300: dt: 0.9000, rms radial error=152.778, avgs=0 150/300: dt: 0.9000, rms radial error=151.929, avgs=0 155/300: dt: 0.9000, rms radial error=151.086, avgs=0 160/300: dt: 0.9000, rms radial error=150.246, avgs=0 165/300: dt: 0.9000, rms radial error=149.411, avgs=0 170/300: dt: 0.9000, rms radial error=148.581, avgs=0 175/300: dt: 0.9000, rms radial error=147.754, avgs=0 180/300: dt: 0.9000, rms radial error=146.933, avgs=0 185/300: dt: 0.9000, rms radial error=146.115, avgs=0 190/300: dt: 0.9000, rms radial error=145.302, avgs=0 195/300: dt: 0.9000, rms radial error=144.493, avgs=0 200/300: dt: 0.9000, rms radial error=143.688, avgs=0 205/300: dt: 0.9000, rms radial error=142.888, avgs=0 210/300: dt: 0.9000, rms radial error=142.091, avgs=0 215/300: dt: 0.9000, rms radial error=141.299, avgs=0 220/300: dt: 0.9000, rms radial error=140.511, avgs=0 225/300: dt: 0.9000, rms radial error=139.727, avgs=0 230/300: dt: 0.9000, rms radial error=138.948, avgs=0 235/300: dt: 0.9000, rms radial error=138.172, avgs=0 240/300: dt: 0.9000, rms radial error=137.401, avgs=0 245/300: dt: 0.9000, rms radial error=136.634, avgs=0 250/300: dt: 0.9000, rms radial error=135.871, avgs=0 255/300: dt: 0.9000, rms radial error=135.112, avgs=0 260/300: dt: 0.9000, rms radial error=134.358, avgs=0 265/300: dt: 0.9000, rms radial error=133.607, avgs=0 270/300: dt: 0.9000, rms radial error=132.860, avgs=0 275/300: dt: 0.9000, rms radial error=132.118, avgs=0 280/300: dt: 0.9000, rms radial error=131.379, avgs=0 285/300: dt: 0.9000, rms radial error=130.645, avgs=0 290/300: dt: 0.9000, rms radial error=129.914, avgs=0 295/300: dt: 0.9000, rms radial error=129.188, avgs=0 300/300: dt: 0.9000, rms radial error=128.465, avgs=0
spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 8624.98 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.02/37 = 0.00056 epoch 2 (K=80.0), pass 1, starting sse = 1491.66 integrating with navgs=32 and tol=3.200e+00 taking m339: dt: 0.29, sse: 1470.4 (0.051, 34.7, 0.000), neg: 26880 (%1.943:%3.54), avgs: 32 340: dt: 0.29, sse: 1470.0 (0.051, 34.7, 0.000), neg: 26948 (%1.935:%3.54), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.68) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.75) 341: dt: 0.29, sse: 1469.7 (0.051, 34.7, 0.000), neg: 27043 (%1.927:%3.55), avgs: 32 342: dt: 0.29, sse: 1469.3 (0.051, 34.7, 0.000), neg: 27089 (%1.919:%3.55), avgs: 32 343: dt: 0.29, sse: 1468.9 (0.051, 34.7, 0.000), neg: 27143 (%1.911:%3.55), avgs: 32 344: dt: 0.29, sse: 1468.5 (0.051, 34.7, 0.000), neg: 27154 (%1.903:%3.55), avgs: 32 345: dt: 0.29, sse: 1467.9 (0.051, 34.7, 0.000), neg: 27168 (%1.892:%3.54), avgs: 32 346: dt: 0.29, sse: 1467.6 (0.051, 34.7, 0.000), neg: 27200 (%1.886:%3.53), avgs: 32 347: dt: 0.29, sse: 1467.3 (0.051, 34.7, 0.000), neg: 27216 (%1.879:%3.53), avgs: 32 348: dt: 0.29, sse: 1466.8 (0.051, 34.7, 0.000), neg: 27228 (%1.870:%3.52), avgs: 32 349: dt: 36.97, sse: 1459.2 (0.051, 34.6, 0.000), neg: 27004 (%1.742:%3.40), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.80) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.79) 350: dt: 4.85, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27064 (%1.688:%3.39), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.81) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.21-->2.79) 351: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27067 (%1.685:%3.39), avgs: 8 352: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27083 (%1.684:%3.39), avgs: 8 353: dt: 0.15, sse: 1455.9 (0.051, 34.6, 0.000), neg: 27080 (%1.681:%3.37), avgs: 8 354: dt: 0.15, sse: 1456.3 (0.051, 34.6, 0.000), neg: 27102 (%1.684:%3.38), avgs: 8 355: dt: 0.15, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27124 (%1.681:%3.37), avgs: 8 356: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27155 (%1.679:%3.37), avgs: 8 357: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27182 (%1.677:%3.36), avgs: 8 358: dt: 0.15, sse: 1456.0 (0.051, 34.6, 0.000), neg: 27190 (%1.674:%3.36), avgs: 8 359: dt: 0.15, sse: 1455.8 (0.051, 34.6, 0.000), neg: 27194 (%1.669:%3.35), avgs: 8 360: dt: 0.15, sse: 1455.6 (0.051, 34.6, 0.000), neg: 27210 (%1.665:%3.35), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.92) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.80) 361: dt: 9.20, sse: 1452.7 (0.051, 34.6, 0.000), neg: 27182 (%1.611:%3.30), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.00) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.80) 362: dt: 0.77, sse: 1451.0 (0.051, 34.6, 0.000), neg: 27300 (%1.582:%3.32), avgs: 2 363: dt: 0.09, sse: 1450.6 (0.051, 34.6, 0.000), neg: 27301 (%1.575:%3.31), avgs: 2 364: dt: 0.09, sse: 1450.3 (0.051, 34.6, 0.000), neg: 27336 (%1.568:%3.31), avgs: 2 365: dt: 0.09, sse: 1449.7 (0.051, 34.6, 0.000), neg: 27352 (%1.556:%3.31), avgs: 2 366: dt: 0.09, sse: 1449.0 (0.051, 34.6, 0.000), neg: 27377 (%1.544:%3.32), avgs: 2 367: dt: 0.09, sse: 1448.6 (0.051, 34.6, 0.000), neg: 27398 (%1.536:%3.31), avgs: 2 368: dt: 0.09, sse: 1448.0 (0.051, 34.6, 0.000), neg: 27412 (%1.526:%3.31), avgs: 2 369: dt: 0.09, sse: 1447.4 (0.051, 34.6, 0.000), neg: 27438 (%1.514:%3.30), avgs: 2 370: dt: 0.09, sse: 1446.5 (0.051, 34.6, 0.000), neg: 27458 (%1.499:%3.30), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.08) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.14-->2.80) 371: dt: 0.09, sse: 1445.8 (0.051, 34.6, 0.000), neg: 27460 (%1.486:%3.29), avgs: 2 372: dt: 0.09, sse: 1445.1 (0.051, 34.6, 0.000), neg: 27497 (%1.474:%3.28), avgs: 2 373: dt: 1.48, sse: 1443.8 (0.051, 34.7, 0.000), neg: 27589 (%1.452:%3.29), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.12-->2.81) 374: dt: 0.27, sse: 1443.2 (0.051, 34.7, 0.000), neg: 27714 (%1.439:%3.27), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.29-->2.81) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
375: dt: 36.63, sse: 250.8 (0.051, 34.6, 0.000), neg: 27421 (%1.349:%3.19), avgs: 32 376: dt: 0.29, sse: 250.5 (0.051, 34.6, 0.000), neg: 27438 (%1.343:%3.19), avgs: 32 377: dt: 0.29, sse: 250.2 (0.051, 34.6, 0.000), neg: 27456 (%1.339:%3.18), avgs: 32 378: dt: 0.29, sse: 249.9 (0.051, 34.6, 0.000), neg: 27450 (%1.333:%3.17), avgs: 32 379: dt: 0.29, sse: 249.6 (0.051, 34.6, 0.000), neg: 27460 (%1.330:%3.16), avgs: 32 380: dt: 0.29, sse: 249.5 (0.051, 34.6, 0.000), neg: 27454 (%1.327:%3.15), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.32-->2.82) 381: dt: 0.29, sse: 249.4 (0.051, 34.6, 0.000), neg: 27446 (%1.325:%3.15), avgs: 32 382: dt: 0.29, sse: 249.2 (0.051, 34.6, 0.000), neg: 27444 (%1.322:%3.14), avgs: 32 383: dt: 0.29, sse: 249.0 (0.051, 34.6, 0.000), neg: 27438 (%1.319:%3.13), avgs: 32 384: dt: 0.29, sse: 248.9 (0.051, 34.6, 0.000), neg: 27421 (%1.317:%3.12), avgs: 32 385: dt: 0.29, sse: 248.7 (0.051, 34.6, 0.000), neg: 27418 (%1.313:%3.12), avgs: 32 386: dt: 155.64, sse: 241.3 (0.051, 34.3, 0.000), neg: 26865 (%1.190:%2.88), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.14) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.26-->2.81) 387: dt: 2.19, sse: 237.7 (0.051, 34.3, 0.000), neg: 26842 (%1.139:%2.86), avgs: 8 388: dt: 0.15, sse: 237.6 (0.051, 34.3, 0.000), neg: 26834 (%1.137:%2.87), avgs: 8 389: dt: 0.15, sse: 237.5 (0.051, 34.3, 0.000), neg: 26828 (%1.136:%2.87), avgs: 8 390: dt: 0.15, sse: 237.2 (0.051, 34.3, 0.000), neg: 26807 (%1.131:%2.86), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.18) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.27-->2.81) 391: dt: 0.15, sse: 236.9 (0.051, 34.3, 0.000), neg: 26807 (%1.126:%2.86), avgs: 8 392: dt: 0.15, sse: 236.5 (0.051, 34.3, 0.000), neg: 26810 (%1.121:%2.86), avgs: 8 393: dt: 0.15, sse: 236.2 (0.051, 34.3, 0.000), neg: 26798 (%1.116:%2.86), avgs: 8 394: dt: 0.15, sse: 235.8 (0.051, 34.3, 0.000), neg: 26789 (%1.110:%2.86), avgs: 8 395: dt: 0.15, sse: 235.5 (0.051, 34.3, 0.000), neg: 26775 (%1.105:%2.86), avgs: 8 396: dt: 0.15, sse: 235.2 (0.051, 34.3, 0.000), neg: 26753 (%1.100:%2.85), avgs: 8 397: dt: 0.15, sse: 234.8 (0.051, 34.3, 0.000), neg: 26743 (%1.094:%2.84), avgs: 8 398: dt: 15.35, sse: 232.1 (0.051, 34.2, 0.000), neg: 26547 (%1.053:%2.76), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.25-->2.82) 399: dt: 1.29, sse: 228.5 (0.051, 34.2, 0.000), neg: 26596 (%1.000:%2.76), avgs: 2 400: dt: 0.54, sse: 227.3 (0.051, 34.2, 0.000), neg: 26618 (%0.983:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.22-->2.82) 401: dt: 0.09, sse: 227.3 (0.051, 34.2, 0.000), neg: 26629 (%0.983:%2.75), avgs: 2 402: dt: 0.09, sse: 227.0 (0.051, 34.2, 0.000), neg: 26613 (%0.978:%2.75), avgs: 2 403: dt: 0.09, sse: 226.7 (0.051, 34.2, 0.000), neg: 26617 (%0.973:%2.76), avgs: 2 404: dt: 0.09, sse: 226.4 (0.051, 34.2, 0.000), neg: 26605 (%0.968:%2.76), avgs: 2 405: dt: 0.09, sse: 226.0 (0.051, 34.2, 0.000), neg: 26603 (%0.962:%2.76), avgs: 2 406: dt: 0.09, sse: 225.8 (0.051, 34.2, 0.000), neg: 26617 (%0.958:%2.77), avgs: 2 407: dt: 0.09, sse: 225.4 (0.051, 34.2, 0.000), neg: 26612 (%0.953:%2.77), avgs: 2 408: dt: 0.09, sse: 225.1 (0.051, 34.2, 0.000), neg: 26604 (%0.948:%2.77), avgs: 2 409: dt: 0.09, sse: 224.8 (0.051, 34.1, 0.000), neg: 26602 (%0.943:%2.76), avgs: 2 410: dt: 0.09, sse: 224.4 (0.051, 34.1, 0.000), neg: 26606 (%0.937:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.35) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 411: dt: 1.71, sse: 223.5 (0.051, 34.1, 0.000), neg: 26591 (%0.925:%2.71), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 412: dt: 0.03, sse: 223.1 (0.051, 34.1, 0.000), neg: 26666 (%0.918:%2.72), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
413: dt: 48.76, sse: 83.1 (0.051, 34.1, 0.000), neg: 26317 (%0.904:%2.68), avgs: 32 414: dt: 0.29, sse: 82.8 (0.051, 34.0, 0.000), neg: 26321 (%0.900:%2.68), avgs: 32 415: dt: 0.29, sse: 82.5 (0.051, 34.0, 0.000), neg: 26315 (%0.895:%2.68), avgs: 32 416: dt: 0.29, sse: 82.1 (0.051, 34.0, 0.000), neg: 26291 (%0.889:%2.67), avgs: 32 417: dt: 0.29, sse: 81.8 (0.051, 34.0, 0.000), neg: 26274 (%0.885:%2.67), avgs: 32 418: dt: 0.29, sse: 81.4 (0.051, 34.0, 0.000), neg: 26258 (%0.880:%2.66), avgs: 32 419: dt: 0.29, sse: 81.0 (0.051, 34.0, 0.000), neg: 26222 (%0.875:%2.65), avgs: 32 420: dt: 0.29, sse: 80.8 (0.051, 34.0, 0.000), neg: 26202 (%0.872:%2.64), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.29) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.84) 421: dt: 0.29, sse: 80.6 (0.051, 34.0, 0.000), neg: 26208 (%0.868:%2.64), avgs: 32 422: dt: 0.29, sse: 80.4 (0.051, 34.0, 0.000), neg: 26186 (%0.866:%2.64), avgs: 32 423: dt: 0.29, sse: 80.2 (0.051, 34.0, 0.000), neg: 26174 (%0.863:%2.64), avgs: 32 424: dt: 42.80, sse: 78.6 (0.051, 34.0, 0.000), neg: 26068 (%0.840:%2.60), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.84) 425: dt: 1.85, sse: 78.2 (0.051, 34.0, 0.000), neg: 26076 (%0.834:%2.57), avgs: 8 426: dt: 0.15, sse: 78.1 (0.051, 34.0, 0.000), neg: 26074 (%0.832:%2.57), avgs: 8 427: dt: 0.15, sse: 77.7 (0.051, 34.0, 0.000), neg: 26071 (%0.828:%2.57), avgs: 8 428: dt: 0.15, sse: 77.6 (0.051, 34.0, 0.000), neg: 26057 (%0.826:%2.57), avgs: 8 429: dt: 0.15, sse: 77.4 (0.051, 33.9, 0.000), neg: 26034 (%0.823:%2.57), avgs: 8 430: dt: 0.15, sse: 76.9 (0.051, 33.9, 0.000), neg: 26021 (%0.817:%2.56), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 431: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26008 (%0.814:%2.57), avgs: 8 432: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26015 (%0.814:%2.58), avgs: 8 433: dt: 0.15, sse: 76.5 (0.051, 33.9, 0.000), neg: 25996 (%0.811:%2.57), avgs: 8 434: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25991 (%0.808:%2.57), avgs: 8 435: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25997 (%0.808:%2.58), avgs: 8 436: dt: 1.20, sse: 76.2 (0.051, 33.9, 0.000), neg: 25992 (%0.805:%2.57), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 437: dt: 1.30, sse: 75.7 (0.051, 33.9, 0.000), neg: 26032 (%0.797:%2.57), avgs: 2 438: dt: 0.09, sse: 75.5 (0.051, 33.9, 0.000), neg: 26022 (%0.795:%2.57), avgs: 2 439: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26010 (%0.789:%2.56), avgs: 2 440: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26003 (%0.788:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.16) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.10-->2.85) 441: dt: 0.09, sse: 74.9 (0.051, 33.9, 0.000), neg: 26008 (%0.786:%2.57), avgs: 2 442: dt: 0.09, sse: 74.7 (0.051, 33.9, 0.000), neg: 26002 (%0.783:%2.57), avgs: 2 443: dt: 0.09, sse: 74.5 (0.051, 33.9, 0.000), neg: 26006 (%0.780:%2.58), avgs: 2 444: dt: 0.09, sse: 74.2 (0.051, 33.9, 0.000), neg: 26014 (%0.775:%2.58), avgs: 2 445: dt: 0.09, sse: 73.9 (0.051, 33.9, 0.000), neg: 26031 (%0.771:%2.58), avgs: 2 446: dt: 0.09, sse: 73.8 (0.051, 33.9, 0.000), neg: 26044 (%0.769:%2.59), avgs: 2 447: dt: 0.09, sse: 73.7 (0.051, 33.9, 0.000), neg: 26058 (%0.767:%2.61), avgs: 2 448: dt: 1.25, sse: 73.3 (0.051, 33.8, 0.000), neg: 25993 (%0.761:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.85) 449: dt: 0.03, sse: 73.2 (0.051, 33.8, 0.000), neg: 26076 (%0.760:%2.60), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.18-->2.85) 449: dt: 0.00, sse: 8423.5 (0.050, 33.8, 0.000), neg: 26076 (%0.754:%2.60), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours omentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.03/37 = 0.00088 epoch 3 (K=320.0), pass 1, starting sse = 256.64 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/38 = 0.00344 epoch 4 (K=1280.0), pass 1, starting sse = 83.95 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/37 = 0.00346 final distance error %100000.00 optimization complete. unfolding took 0.12 hours #-------------------------------------------- #@# Fix Topology lh Wed Mar 3 22:34:46 CET 2010
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/home/kutato/freesurfer/subjects/C1/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga C1 lh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters
Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ before topology correction, eno=-408 (nv=152952, nf=306720, ne=460080, g=205) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 56276 ambiguous faces found in tessellation segmenting defects... 92 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 4 -merging segment 0 into 5 -merging segment 29 into 27 -merging segment 32 into 30 -merging segment 71 into 49 -merging segment 4 into 52 -merging segment 74 into 72 85 defects to be corrected 0 vertices coincident reading input surface /home/kutato/freesurfer/subjects/C1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1015 (-4.5508) -vertex loglikelihood: -6.5092 (-3.2546) -normal dot loglikelihood: -3.5881 (-3.5881) -quad curv loglikelihood: -5.9652 (-2.9826) Total Loglikelihood : -25.1641
CORRECTING DEFECT 0 (vertices=48, convex hull=73) After retessellation of defect 0, euler #=-66 (121738,358994,237190) : difference with theory (-82) = -16
CORRECTING DEFECT 1 (vertices=172, convex hull=59) After retessellation of defect 1, euler #=-65 (121763,359092,237264) : difference with theory (-81) = -16
CORRECTING DEFECT 2 (vertices=14, convex hull=14) After retessellation of defect 2, euler #=-64 (121763,359095,237268) : difference with theory (-80) = -16
CORRECTING DEFECT 3 (vertices=4413, convex hull=721) After retessellation of defect 3, euler #=-67 (122638,362153,239448) : difference with theory (-79) = -12
CORRECTING DEFECT 4 (vertices=16, convex hull=21) After retessellation of defect 4, euler #=-66 (122639,362162,239457) : difference with theory (-78) = -12
CORRECTING DEFECT 5 (vertices=318, convex hull=123) After retessellation of defect 5, euler #=-65 (122682,362353,239606) : difference with theory (-77) = -12
CORRECTING DEFECT 6 (vertices=39, convex hull=81) After retessellation of defect 6, euler #=-64 (122698,362433,239671) : difference with theory (-76) = -12
CORRECTING DEFECT 7 (vertices=43, convex hull=30) After retessellation of defect 7, euler #=-63 (122702,362458,239693) : difference with theory (-75) = -12
CORRECTING DEFECT 8 (vertices=87, convex hull=103) After retessellation of defect 8, euler #=-62 (122736,362601,239803) : difference with theory (-74) = -12
CORRECTING DEFECT 9 (vertices=22, convex hull=52) After retessellation of defect 9, euler #=-61 (122744,362644,239839) : difference with theory (-73) = -12
CORRECTING DEFECT 10 (vertices=103, convex hull=78) After retessellation of defect 10, euler #=-60 (122768,362752,239924) : difference with theory (-72) = -12
CORRECTING DEFECT 11 (vertices=427, convex hull=253) After retessellation of defect 11, euler #=-59 (122927,363356,240370) : difference with theory (-71) = -12
CORRECTING DEFECT 12 (vertices=1508, convex hull=562) After retessellation of defect 12, euler #=-59 (123340,364897,241498) : difference with theory (-70) = -11
CORRECTING DEFECT 13 (vertices=57, convex hull=109) After retessellation of defect 13, euler #=-58 (123374,365043,241611) : difference with theory (-69) = -11
CORRECTING DEFECT 14 (vertices=49, convex hull=79) After retessellation of defect 14, euler #=-57 (123402,365159,241700) : difference with theory (-68) = -11
CORRECTING DEFECT 15 (vertices=69, convex hull=96) After retessellation of defect 15, euler #=-56 (123431,365288,241801) : difference with theory (-67) = -11
CORRECTING DEFECT 16 (vertices=29, convex hull=55) After retessellation of defect 16, euler #=-55 (123440,365339,241844) : difference with theory (-66) = -11
CORRECTING DEFECT 17 (vertices=14, convex hull=28) After retessellation of defect 17, euler #=-54 (123443,365354,241857) : difference with theory (-65) = -11
CORRECTING DEFECT 18 (vertices=41, convex hull=48) After retessellation of defect 18, euler #=-53 (123452,365398,241893) : difference with theory (-64) = -11
CORRECTING DEFECT 19 (vertices=459, convex hull=241) After retessellation of defect 19, euler #=-52 (123590,365935,242293) : difference with theory (-63) = -11
CORRECTING DEFECT 20 (vertices=55, convex hull=110) After retessellation of defect 20, euler #=-51 (123623,366080,242406) : difference with theory (-62) = -11
CORRECTING DEFECT 21 (vertices=478, convex hull=255) After retessellation of defect 21, euler #=-50 (123653,366319,242616) : difference with theory (-61) = -11
CORRECTING DEFECT 22 (vertices=27, convex hull=34) After retessellation of defect 22, euler #=-49 (123662,366357,242646) : difference with theory (-60) = -11
CORRECTING DEFECT 23 (vertices=53, convex hull=92) After retessellation of defect 23, euler #=-48 (123692,366487,242747) : difference with theory (-59) = -11
CORRECTING DEFECT 24 (vertices=32, convex hull=45) After retessellation of defect 24, euler #=-46 (123692,366504,242766) : difference with theory (-58) = -12
CORRECTING DEFECT 25 (vertices=181, convex hull=167) After retessellation of defect 25, euler #=-45 (123711,366644,242888) : difference with theory (-57) = -12
CORRECTING DEFECT 26 (vertices=1122, convex hull=340) After retessellation of defect 26, euler #=-45 (124058,367886,243783) : difference with theory (-56) = -11
CORRECTING DEFECT 27 (vertices=213, convex hull=67) After retessellation of defect 27, euler #=-44 (124080,367986,243862) : difference with theory (-55) = -11
CORRECTING DEFECT 28 (vertices=35, convex hull=22) After retessellation of defect 28, euler #=-43 (124085,368007,243879) : difference with theory (-54) = -11
CORRECTING DEFECT 29 (vertices=20, convex hull=63) After retessellation of defect 29, euler #=-42 (124095,368059,243922) : difference with theory (-53) = -11
CORRECTING DEFECT 30 (vertices=13, convex hull=26) After retessellation of defect 30, euler #=-41 (124096,368072,243935) : difference with theory (-52) = -11
CORRECTING DEFECT 31 (vertices=29, convex hull=74) After retessellation of defect 31, euler #=-40 (124105,368127,243982) : difference with theory (-51) = -11
CORRECTING DEFECT 32 (vertices=42, convex hull=33) After retessellation of defect 32, euler #=-39 (124109,368148,244000) : difference with theory (-50) = -11
CORRECTING DEFECT 33 (vertices=88, convex hull=93) After retessellation of defect 33, euler #=-38 (124124,368233,244071) : difference with theory (-49) = -11
CORRECTING DEFECT 34 (vertices=53, convex hull=67) After retessellation of defect 34, euler #=-37 (124137,368300,244126) : difference with theory (-48) = -11
CORRECTING DEFECT 35 (vertices=396, convex hull=152) After retessellation of defect 35, euler #=-36 (124283,368807,244488) : difference with theory (-47) = -11
CORRECTING DEFECT 36 (vertices=49, convex hull=71) After retessellation of defect 36, euler #=-35 (124310,368918,244573) : difference with theory (-46) = -11
CORRECTING DEFECT 37 (vertices=6, convex hull=20) After retessellation of defect 37, euler #=-34 (124311,368926,244581) : difference with theory (-45) = -11
CORRECTING DEFECT 38 (vertices=42, convex hull=81) After retessellation of defect 38, euler #=-33 (124337,369038,244668) : difference with theory (-44) = -11
CORRECTING DEFECT 39 (vertices=96, convex hull=66) After retessellation of defect 39, euler #=-32 (124378,369192,244782) : difference with theory (-43) = -11
CORRECTING DEFECT 40 (vertices=27, convex hull=34) After retessellation of defect 40, euler #=-31 (124382,369214,244801) : difference with theory (-42) = -11
CORRECTING DEFECT 41 (vertices=295, convex hull=174) After retessellation of defect 41, euler #=-30 (124455,369519,245034) : difference with theory (-41) = -11
CORRECTING DEFECT 42 (vertices=192, convex hull=126) After retessellation of defect 42, euler #=-29 (124483,369662,245150) : difference with theory (-40) = -11
CORRECTING DEFECT 43 (vertices=100, convex hull=110) After retessellation of defect 43, euler #=-28 (124549,369912,245335) : difference with theory (-39) = -11
CORRECTING DEFECT 44 (vertices=564, convex hull=398) After retessellation of defect 44, euler #=-27 (124766,370766,245973) : difference with theory (-38) = -11
CORRECTING DEFECT 45 (vertices=148, convex hull=121) After retessellation of defect 45, euler #=-26 (124843,371049,246180) : difference with theory (-37) = -11
CORRECTING DEFECT 46 (vertices=51, convex hull=75) After retessellation of defect 46, euler #=-25 (124855,371114,246234) : difference with theory (-36) = -11
CORRECTING DEFECT 47 (vertices=16122, convex hull=4397) normal vector of length zero at vertex 139578 with 0 faces vertex 139578 has 0 face Numerical result out of range Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 4 05:39:45 CET 2010
2010/3/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Gabor,
recon2-cp currently starts *after* the aseg, so you'll need to rerun it from an ealier point than that. Try using -autorecon2 instead.
cheers Bruce
On Wed, 3 Mar 2010, Perlaki Gabor wrote:
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all!
We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised.
We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later.
Could anyone help us in this?
And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity).
And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ).
Thank you very much.
Gergely Orsi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
Hi Gabor,
we'd have to look at the dataset, but usually if you put points in the cerebellar wm it will help the gm segmentation. If you want to upload the dataset we'll take a look.
cheers Bruce On Thu, 4 Mar 2010, Perlaki Gabor wrote:
Hi Bruce,
Then the problem is that we put the points in the cerebellum gray matter because we miss that part of cerebellum. Is there any method to correct the gray matter somehow?
Thanks a lot, Gabor
On Thu, 4 Mar 2010 09:01:48 -0500 (EST), Bruce Fischl wrote
hmmm, looks like there is a huge defect in the surface. Did you look at them to make sure nothing is very wrong (e.g. cerebellum attached to cortex)? Make sure you didn't include any control points in cerebellar gray matter, only in points that are in the interior of the white matter (and not for example in the dentate)
cheers, Bruce
On Thu, 4 Mar 2010, Gergely Orsi wrote:
Hi Bruce,
Thanks for your help. I've run the recon-all as you told (recon-all -autorecon2 -autorecon3 -subjid C1), but the recon-all exited with errors. I'm sending you the log. Could you help us some more?
Thank you.
Gergely Orsi
New invocation of recon-all
Wed Mar 3 16:00:17 CET 2010 /home/kutato/freesurfer/subjects/C1 /home/kutato/freesurfer/bin/recon-all -autorecon2 -autorecon3 -subjid C1 subjid C1 setenv SUBJECTS_DIR /home/kutato/freesurfer/subjects FREESURFER_HOME /home/kutato/freesurfer Actual FREESURFER_HOME /home/kutato/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cachedMem: 4020216 2044228 1975988 0 182484 1237240 Swap: 8634360 0 8634360
######################################## program versions used $Id: recon-all,v 1.133.2.38 2009/01/08 19:49:55 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: tkregister2.c,v 1.86.2.7 2009/01/18 19:41:35 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_ca_label.c,v 1.80.2.5 2008/08/15 21:00:02 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:17-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.5 2009/01/15 01:36:52 greve Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/03/03-15:00:18-GMT BuildTimeStamp: Jan 19 2009 07:14:08 CVS: $Id: mris_curvature_stats.c,v 1.28.2.4 2008/10/02 21:42:03 nicks Exp $ User: kutato Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.29.4-167.fc11.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #------------------------------------- #@# EM Registration Wed Mar 3 16:00:18 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_em_register -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros)
spacing=8, using 2185 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 initial log_p = -84452.9
First Search limited to translation only.
Found translation: (-0.3, -12.2, -22.4): log p = -24312.3
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-24312.3 (thresh=-24288.0) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-12644.5, old_max_log_p =-12644.5 (thresh=-12631.8) 1.052 0.008 -0.061 -0.229; 0.000 1.185 0.156 -56.411; 0.074 -0.130 0.989 -13.358; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-12036.9, old_max_log_p =-12644.5 (thresh=-12631.8) 1.067 -0.009 -0.080 4.483; 0.020 1.198 0.188 -64.729; 0.090 -0.169 0.966 -5.663; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11905.9, old_max_log_p =-12036.9 (thresh=-12024.8) 1.050 -0.009 -0.079 6.394; 0.021 1.195 0.204 -66.521; 0.089 -0.185 0.948 -0.958; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-11904.4, old_max_log_p =-11905.9 (thresh=-11894.0) 1.050 0.011 -0.076 3.377; 0.004 1.214 0.208 -67.391; 0.090 -0.188 0.963 -2.618; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11904.4 (thresh=-11892.5) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-11516.2, old_max_log_p =-11516.2 (thresh=-11504.7) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 2185 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 11516.2 tol 0.000010 Resulting transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -11516.2 (old=-84452.9) transform before final EM align: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 244171 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.05627 -0.00843 -0.05454 1.60147; 0.01542 1.20280 0.18920 -64.93600; 0.06466 -0.16904 0.97149 -3.01754; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1559944.8 tol 0.000000 final transform: 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta... registration took 38 minutes and 54 seconds. #-------------------------------------- #@# CA Normalize Wed Mar 3 16:39:12 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -mask brainmask.mgz nu.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
reading manually defined control points from /home/kutato/freesurfer/subjects/C1/tmp/control.dat using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=35.9 skull bounding box = (59, 73, 41) --> (190, 189, 221) using (103, 112, 131) as brain centroid... mean wm in atlas = 107, using box (87,98,109) --> (119, 126,153) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 141, scaling input intensities by 0.759 scaling channel 0 by 0.758865 using 244171 sample points... INFO: compute sample coordinates transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 109.0 164 of 520 (31.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 112.0 208 of 519 (40.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 117.0 3 of 14 (21.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 121.0 4 of 21 (19.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 101.0 --> 116.0 6 of 51 (11.8%) samples deleted using 1125 total control points for intensity normalization... bias field = 1.011 +- 0.076 0 of 1450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 171 of 491 (34.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 113.0 132 of 559 (23.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 116.0 16 of 67 (23.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 117.0 10 of 70 (14.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 99.0 --> 113.0 12 of 94 (12.8%) samples deleted using 1281 total control points for intensity normalization... bias field = 0.994 +- 0.088 0 of 1650 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 76, 47) --> (187, 170, 215) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 110.0 210 of 555 (37.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 78, 48) --> (128, 170, 217) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 168 of 597 (28.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 149, 73) --> (172, 186, 128) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 113.0 21 of 79 (26.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 149, 73) --> (125, 185, 130) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 113.0 19 of 85 (22.4%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 109) --> (141, 198, 141) Reading 710 control points... Brain_Stem: limiting intensities to 91.0 --> 106.0 64 of 179 (35.8%) samples deleted using 1495 total control points for intensity normalization... bias field = 0.997 +- 0.082 0 of 1723 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Wed Mar 3 16:40:49 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/kutato/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.27 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.766, neg=0, invalid=766 0001: dt=228.525253, rms=0.731 (4.651%), neg=0, invalid=766 0002: dt=230.826667, rms=0.716 (1.976%), neg=0, invalid=766 0003: dt=131.235955, rms=0.711 (0.775%), neg=0, invalid=766 0004: dt=369.920000, rms=0.705 (0.719%), neg=0, invalid=766 0005: dt=134.901961, rms=0.702 (0.467%), neg=0, invalid=766 0006: dt=295.936000, rms=0.700 (0.338%), neg=0, invalid=766 0007: dt=129.472000, rms=0.698 (0.295%), neg=0, invalid=766 0008: dt=443.904000, rms=0.696 (0.269%), neg=0, invalid=766 0009: dt=142.933333, rms=0.694 (0.331%), neg=0, invalid=766 0010: dt=129.472000, rms=0.693 (0.073%), neg=0, invalid=766 0011: dt=129.472000, rms=0.692 (0.120%), neg=0, invalid=766 0012: dt=129.472000, rms=0.691 (0.183%), neg=0, invalid=766 0013: dt=129.472000, rms=0.689 (0.236%), neg=0, invalid=766 0014: dt=129.472000, rms=0.688 (0.265%), neg=0, invalid=766 0015: dt=129.472000, rms=0.686 (0.290%), neg=0, invalid=766 0016: dt=129.472000, rms=0.684 (0.282%), neg=0, invalid=766 0017: dt=129.472000, rms=0.682 (0.255%), neg=0, invalid=766 0018: dt=129.472000, rms=0.680 (0.239%), neg=0, invalid=766 0019: dt=129.472000, rms=0.679 (0.216%), neg=0, invalid=766 0020: dt=129.472000, rms=0.677 (0.204%), neg=0, invalid=766 0021: dt=129.472000, rms=0.676 (0.193%), neg=0, invalid=766 0022: dt=129.472000, rms=0.675 (0.166%), neg=0, invalid=766 0023: dt=129.472000, rms=0.674 (0.165%), neg=0, invalid=766 0024: dt=129.472000, rms=0.673 (0.171%), neg=0, invalid=766 0025: dt=129.472000, rms=0.672 (0.159%), neg=0, invalid=766 0026: dt=129.472000, rms=0.671 (0.137%), neg=0, invalid=766 0027: dt=129.472000, rms=0.670 (0.106%), neg=0, invalid=766 0028: dt=129.472000, rms=0.669 (0.111%), neg=0, invalid=766 0029: dt=129.472000, rms=0.668 (0.128%), neg=0, invalid=766 0030: dt=129.472000, rms=0.668 (0.109%), neg=0, invalid=766 0031: dt=129.472000, rms=0.667 (0.086%), neg=0, invalid=766 0032: dt=517.888000, rms=0.667 (0.023%), neg=0, invalid=766 0033: dt=517.888000, rms=0.667 (0.014%), neg=0, invalid=766 0034: dt=517.888000, rms=0.667 (-1.199%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0035: dt=129.472000, rms=0.665 (0.222%), neg=0, invalid=766 0036: dt=517.888000, rms=0.664 (0.233%), neg=0, invalid=766 0037: dt=129.472000, rms=0.664 (0.033%), neg=0, invalid=766 0038: dt=129.472000, rms=0.663 (0.026%), neg=0, invalid=766 0039: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0040: dt=129.472000, rms=0.663 (0.045%), neg=0, invalid=766 0041: dt=129.472000, rms=0.662 (0.070%), neg=0, invalid=766 0042: dt=129.472000, rms=0.662 (0.085%), neg=0, invalid=766 0043: dt=129.472000, rms=0.661 (0.081%), neg=0, invalid=766 0044: dt=129.472000, rms=0.661 (0.066%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 0045: dt=134.243902, rms=0.662 (0.847%), neg=0, invalid=766 0046: dt=136.900662, rms=0.651 (1.582%), neg=0, invalid=766 0047: dt=38.171429, rms=0.648 (0.467%), neg=0, invalid=766 0048: dt=145.152000, rms=0.645 (0.545%), neg=0, invalid=766 0049: dt=115.559395, rms=0.639 (0.880%), neg=0, invalid=766 0050: dt=36.288000, rms=0.638 (0.223%), neg=0, invalid=766 0051: dt=36.288000, rms=0.637 (0.131%), neg=0, invalid=766 0052: dt=36.288000, rms=0.635 (0.241%), neg=0, invalid=766 0053: dt=36.288000, rms=0.633 (0.377%), neg=0, invalid=766 0054: dt=36.288000, rms=0.630 (0.495%), neg=0, invalid=766 0055: dt=36.288000, rms=0.626 (0.531%), neg=0, invalid=766 0056: dt=36.288000, rms=0.623 (0.511%), neg=0, invalid=766 0057: dt=36.288000, rms=0.620 (0.485%), neg=0, invalid=766 0058: dt=36.288000, rms=0.617 (0.438%), neg=0, invalid=766 0059: dt=36.288000, rms=0.615 (0.421%), neg=0, invalid=766 0060: dt=36.288000, rms=0.612 (0.398%), neg=0, invalid=766 0061: dt=36.288000, rms=0.610 (0.353%), neg=0, invalid=766 0062: dt=36.288000, rms=0.609 (0.288%), neg=0, invalid=766 0063: dt=36.288000, rms=0.607 (0.241%), neg=0, invalid=766 0064: dt=36.288000, rms=0.606 (0.222%), neg=0, invalid=766 0065: dt=36.288000, rms=0.604 (0.208%), neg=0, invalid=766 0066: dt=36.288000, rms=0.603 (0.189%), neg=0, invalid=766 0067: dt=36.288000, rms=0.602 (0.167%), neg=0, invalid=766 0068: dt=36.288000, rms=0.601 (0.138%), neg=0, invalid=766 0069: dt=36.288000, rms=0.601 (0.134%), neg=0, invalid=766 0070: dt=36.288000, rms=0.600 (0.136%), neg=0, invalid=766 0071: dt=36.288000, rms=0.599 (0.142%), neg=0, invalid=766 0072: dt=36.288000, rms=0.598 (0.122%), neg=0, invalid=766 0073: dt=36.288000, rms=0.598 (0.110%), neg=0, invalid=766 0074: dt=124.416000, rms=0.597 (0.030%), neg=0, invalid=766 0075: dt=124.416000, rms=0.597 (-0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0076: dt=97.215190, rms=0.596 (0.268%), neg=0, invalid=766 0077: dt=37.647059, rms=0.595 (0.061%), neg=0, invalid=766 0078: dt=37.647059, rms=0.595 (0.033%), neg=0, invalid=766 0079: dt=37.647059, rms=0.595 (0.049%), neg=0, invalid=766 0080: dt=37.647059, rms=0.595 (0.050%), neg=0, invalid=766 0081: dt=37.647059, rms=0.594 (0.046%), neg=0, invalid=766 0082: dt=37.647059, rms=0.594 (0.028%), neg=0, invalid=766 0083: dt=36.288000, rms=0.594 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.59 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0084: dt=4.000000, rms=0.621 (0.022%), neg=0, invalid=766 0085: dt=1.600000, rms=0.621 (0.002%), neg=0, invalid=766 0086: dt=1.600000, rms=0.621 (0.001%), neg=0, invalid=766 0087: dt=1.600000, rms=0.621 (-0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=766 0088: dt=1.600000, rms=0.621 (0.003%), neg=0, invalid=766 0089: dt=0.175000, rms=0.621 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0090: dt=5.778409, rms=0.671 (3.273%), neg=0, invalid=766 0091: dt=4.807692, rms=0.668 (0.356%), neg=0, invalid=766 0092: dt=2.304000, rms=0.668 (0.026%), neg=0, invalid=766 0093: dt=2.304000, rms=0.668 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 0094: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 0095: dt=0.384000, rms=0.717 (0.063%), neg=0, invalid=766 0096: dt=0.514706, rms=0.717 (0.077%), neg=0, invalid=766 0097: dt=1.280000, rms=0.716 (0.178%), neg=0, invalid=766 0098: dt=2.622951, rms=0.712 (0.483%), neg=0, invalid=766 0099: dt=0.448000, rms=0.712 (0.022%), neg=0, invalid=766 0100: dt=0.448000, rms=0.712 (0.029%), neg=0, invalid=766 0101: dt=0.448000, rms=0.711 (0.051%), neg=0, invalid=766 0102: dt=0.448000, rms=0.711 (0.065%), neg=0, invalid=766 0103: dt=0.448000, rms=0.711 (0.069%), neg=0, invalid=766 0104: dt=0.448000, rms=0.710 (0.049%), neg=0, invalid=766 0105: dt=0.448000, rms=0.710 (0.002%), neg=0, invalid=766 0106: dt=1.280000, rms=0.710 (0.013%), neg=0, invalid=766 0107: dt=3.307692, rms=0.709 (0.091%), neg=0, invalid=766 0108: dt=0.384000, rms=0.709 (0.016%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=766 0109: dt=1.024000, rms=0.709 (0.098%), neg=0, invalid=766 0110: dt=0.000000, rms=0.709 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=766 0111: dt=0.768240, rms=0.672 (2.434%), neg=0, invalid=766 0112: dt=0.028000, rms=0.671 (0.144%), neg=0, invalid=766 0113: dt=0.028000, rms=0.671 (-0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.671, neg=0, invalid=766 0114: dt=0.016000, rms=0.670 (0.020%), neg=0, invalid=766 0115: dt=0.000000, rms=0.670 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13848 (32) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (3561 voxels, peak = 31), gca=30.6 gca peak = 0.14022 (22) mri peak = 0.14987 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, overlap=0.258) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (3059 voxels, peak = 31), gca=31.3 gca peak = 0.24234 (100) mri peak = 0.17616 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (559 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.15860 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, overlap=0.633) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (537 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.09927 (79) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1161 voxels, peak = 77), gca=77.2 gca peak = 0.29892 (64) mri peak = 0.08177 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, overlap=0.005) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1295 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.06542 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (93940 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.05686 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (98701 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.02314 (77) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (63871 voxels, peak = 80), gca=80.3 gca peak = 0.13270 (63) mri peak = 0.02476 (84) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (62517 voxels, peak = 77), gca=77.2 gca peak = 0.15182 (70) mri peak = 0.16579 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.17 x + 0.0 (789 voxels, peak = 82), gca=82.2 gca peak = 0.14251 (76) mri peak = 0.22639 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, overlap=0.339) Left_Caudate (11): linear fit = 1.12 x + 0.0 (871 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.02272 (74) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (33059 voxels, peak = 80), gca=79.5 gca peak = 0.12723 (61) mri peak = 0.02272 (77) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (35568 voxels, peak = 82), gca=82.3 gca peak = 0.22684 (88) mri peak = 0.06491 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (11517 voxels, peak = 112), gca=112.2 gca peak = 0.21067 (87) mri peak = 0.06839 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (10222 voxels, peak = 109), gca=108.8 gca peak = 0.25455 (62) mri peak = 0.16005 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (415 voxels, peak = 78), gca=77.5 gca peak = 0.39668 (62) mri peak = 0.19364 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (421 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.08041 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, overlap=0.801) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5834 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.08539 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, overlap=0.548) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5169 voxels, peak = 98), gca=97.9 gca peak = 0.13716 (82) mri peak = 0.09766 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, overlap=0.375) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2963 voxels, peak = 92), gca=92.2 gca peak = 0.15214 (84) mri peak = 0.10719 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, overlap=0.371) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2862 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.08349 (101) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, overlap=0.001) Brain_Stem (16): linear fit = 1.20 x + 0.0 (14919 voxels, peak = 102), gca=102.0 gca peak = 0.11809 (92) mri peak = 0.09947 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1686 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07866 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1860 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.19514 (33) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, overlap=0.860) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (147 voxels, peak = 32), gca=32.4 gca peak = 0.13542 (27) mri peak = 0.12763 (32) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, overlap=0.418) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (691 voxels, peak = 34), gca=34.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.22 x + 0.0 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... 0000: dt=0.000, rms=0.693, neg=0, invalid=766 0116: dt=108.542373, rms=0.671 (3.115%), neg=0, invalid=766 0117: dt=247.972125, rms=0.664 (1.098%), neg=0, invalid=766 0118: dt=192.927536, rms=0.659 (0.715%), neg=0, invalid=766 0119: dt=87.482014, rms=0.657 (0.292%), neg=0, invalid=766 0120: dt=517.888000, rms=0.653 (0.661%), neg=0, invalid=766 0121: dt=77.748148, rms=0.651 (0.220%), neg=0, invalid=766 0122: dt=2071.552000, rms=0.643 (1.306%), neg=0, invalid=766 0123: dt=71.896869, rms=0.640 (0.383%), neg=0, invalid=766 0124: dt=129.472000, rms=0.640 (0.109%), neg=0, invalid=766 0125: dt=517.888000, rms=0.637 (0.376%), neg=0, invalid=766 0126: dt=73.984000, rms=0.637 (0.062%), neg=0, invalid=766 0127: dt=887.808000, rms=0.635 (0.288%), neg=0, invalid=766 0128: dt=129.472000, rms=0.634 (0.235%), neg=0, invalid=766 0129: dt=517.888000, rms=0.633 (0.150%), neg=0, invalid=766 0130: dt=129.472000, rms=0.632 (0.119%), neg=0, invalid=766 0131: dt=295.936000, rms=0.631 (0.082%), neg=0, invalid=766 0132: dt=129.472000, rms=0.631 (0.085%), neg=0, invalid=766 0133: dt=221.952000, rms=0.630 (0.065%), neg=0, invalid=766 0134: dt=129.472000, rms=0.630 (0.073%), neg=0, invalid=766 0135: dt=295.936000, rms=0.630 (0.058%), neg=0, invalid=766 0136: dt=129.472000, rms=0.629 (0.094%), neg=0, invalid=766 0137: dt=110.976000, rms=0.629 (0.022%), neg=0, invalid=766 0138: dt=110.976000, rms=0.629 (0.053%), neg=0, invalid=766 0139: dt=110.976000, rms=0.628 (0.073%), neg=0, invalid=766 0140: dt=110.976000, rms=0.628 (0.081%), neg=0, invalid=766 0141: dt=110.976000, rms=0.627 (0.103%), neg=0, invalid=766 0142: dt=110.976000, rms=0.626 (0.149%), neg=0, invalid=766 0143: dt=110.976000, rms=0.625 (0.151%), neg=0, invalid=766 0144: dt=110.976000, rms=0.624 (0.152%), neg=0, invalid=766 0145: dt=110.976000, rms=0.623 (0.156%), neg=0, invalid=766 0146: dt=110.976000, rms=0.622 (0.160%), neg=0, invalid=766 0147: dt=110.976000, rms=0.621 (0.164%), neg=0, invalid=766 0148: dt=110.976000, rms=0.620 (0.157%), neg=0, invalid=766 0149: dt=110.976000, rms=0.619 (0.155%), neg=0, invalid=766 0150: dt=110.976000, rms=0.618 (0.154%), neg=0, invalid=766 0151: dt=110.976000, rms=0.617 (0.144%), neg=0, invalid=766 0152: dt=110.976000, rms=0.617 (0.122%), neg=0, invalid=766 0153: dt=110.976000, rms=0.616 (0.134%), neg=0, invalid=766 0154: dt=110.976000, rms=0.615 (0.147%), neg=0, invalid=766 0155: dt=110.976000, rms=0.614 (0.136%), neg=0, invalid=766 0156: dt=110.976000, rms=0.613 (0.119%), neg=0, invalid=766 0157: dt=110.976000, rms=0.613 (0.094%), neg=0, invalid=766 0158: dt=110.976000, rms=0.612 (0.112%), neg=0, invalid=766 0159: dt=110.976000, rms=0.611 (0.119%), neg=0, invalid=766 0160: dt=110.976000, rms=0.611 (0.098%), neg=0, invalid=766 0161: dt=110.976000, rms=0.610 (0.070%), neg=0, invalid=766 0162: dt=110.976000, rms=0.610 (0.093%), neg=0, invalid=766 0163: dt=110.976000, rms=0.609 (0.101%), neg=0, invalid=766 0164: dt=110.976000, rms=0.609 (0.086%), neg=0, invalid=766 0165: dt=110.976000, rms=0.608 (0.069%), neg=0, invalid=766 0166: dt=110.976000, rms=0.608 (0.081%), neg=0, invalid=766 0167: dt=110.976000, rms=0.607 (0.080%), neg=0, invalid=766 0168: dt=110.976000, rms=0.607 (0.067%), neg=0, invalid=766 0169: dt=110.976000, rms=0.606 (0.054%), neg=0, invalid=766 0170: dt=110.976000, rms=0.606 (0.060%), neg=0, invalid=766 0171: dt=110.976000, rms=0.606 (0.064%), neg=0, invalid=766 0172: dt=110.976000, rms=0.605 (0.066%), neg=0, invalid=766 0173: dt=110.976000, rms=0.605 (0.054%), neg=0, invalid=766 0174: dt=110.976000, rms=0.605 (0.053%), neg=0, invalid=766 0175: dt=110.976000, rms=0.604 (0.052%), neg=0, invalid=766 0176: dt=110.976000, rms=0.604 (0.048%), neg=0, invalid=766 0177: dt=110.976000, rms=0.604 (0.045%), neg=0, invalid=766 0178: dt=110.976000, rms=0.604 (0.043%), neg=0, invalid=766 0179: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=766 0180: dt=110.976000, rms=0.603 (0.050%), neg=0, invalid=766 0181: dt=110.976000, rms=0.603 (0.047%), neg=0, invalid=766 0182: dt=110.976000, rms=0.602 (0.035%), neg=0, invalid=766 0183: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=766 0184: dt=110.976000, rms=0.602 (0.040%), neg=0, invalid=766 0185: dt=110.976000, rms=0.602 (0.037%), neg=0, invalid=766 0186: dt=110.976000, rms=0.602 (0.033%), neg=0, invalid=766 0187: dt=110.976000, rms=0.601 (0.037%), neg=0, invalid=766 0188: dt=110.976000, rms=0.601 (0.030%), neg=0, invalid=766 0189: dt=110.976000, rms=0.601 (0.035%), neg=0, invalid=766 0190: dt=110.976000, rms=0.601 (0.040%), neg=0, invalid=766 0191: dt=110.976000, rms=0.601 (0.031%), neg=0, invalid=766 0192: dt=110.976000, rms=0.600 (0.027%), neg=0, invalid=766 0193: dt=110.976000, rms=0.600 (0.038%), neg=0, invalid=766 0194: dt=110.976000, rms=0.600 (0.035%), neg=0, invalid=766 0195: dt=110.976000, rms=0.600 (0.023%), neg=0, invalid=766 0196: dt=110.976000, rms=0.600 (0.028%), neg=0, invalid=766 0197: dt=110.976000, rms=0.599 (0.032%), neg=0, invalid=766 0198: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0199: dt=110.976000, rms=0.599 (0.027%), neg=0, invalid=766 0200: dt=110.976000, rms=0.599 (0.026%), neg=0, invalid=766 0201: dt=110.976000, rms=0.599 (0.030%), neg=0, invalid=766 0202: dt=110.976000, rms=0.599 (0.028%), neg=0, invalid=766 0203: dt=110.976000, rms=0.598 (0.022%), neg=0, invalid=766 0204: dt=110.976000, rms=0.598 (0.032%), neg=0, invalid=766 0205: dt=110.976000, rms=0.598 (0.028%), neg=0, invalid=766 0206: dt=110.976000, rms=0.598 (0.021%), neg=0, invalid=766 0207: dt=110.976000, rms=0.598 (0.023%), neg=0, invalid=766 0208: dt=110.976000, rms=0.598 (0.024%), neg=0, invalid=766 0209: dt=110.976000, rms=0.598 (0.025%), neg=0, invalid=766 0210: dt=110.976000, rms=0.597 (0.020%), neg=0, invalid=766 0211: dt=221.952000, rms=0.597 (0.001%), neg=0, invalid=766 0212: dt=221.952000, rms=0.597 (0.014%), neg=0, invalid=766 0213: dt=221.952000, rms=0.597 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=766 0214: dt=221.952000, rms=0.597 (0.077%), neg=0, invalid=766 0215: dt=443.904000, rms=0.596 (0.152%), neg=0, invalid=766 0216: dt=32.368000, rms=0.596 (0.018%), neg=0, invalid=766 0217: dt=32.368000, rms=0.596 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 0218: dt=112.375587, rms=0.596 (0.426%), neg=0, invalid=766 0219: dt=67.729134, rms=0.592 (0.773%), neg=0, invalid=766 0220: dt=31.104000, rms=0.590 (0.211%), neg=0, invalid=766 0221: dt=580.608000, rms=0.577 (2.307%), neg=0, invalid=766 0222: dt=64.000000, rms=0.574 (0.535%), neg=0, invalid=766 0223: dt=25.920000, rms=0.573 (0.091%), neg=0, invalid=766 0224: dt=331.776000, rms=0.571 (0.410%), neg=0, invalid=766 0225: dt=50.070588, rms=0.568 (0.559%), neg=0, invalid=766 0226: dt=20.736000, rms=0.567 (0.042%), neg=0, invalid=766 0227: dt=20.736000, rms=0.567 (0.035%), neg=0, invalid=766 0228: dt=20.736000, rms=0.567 (0.064%), neg=0, invalid=766 0229: dt=20.736000, rms=0.566 (0.111%), neg=0, invalid=766 0230: dt=20.736000, rms=0.565 (0.159%), neg=0, invalid=766 0231: dt=20.736000, rms=0.564 (0.176%), neg=0, invalid=766 0232: dt=20.736000, rms=0.563 (0.180%), neg=0, invalid=766 0233: dt=20.736000, rms=0.562 (0.180%), neg=0, invalid=766 0234: dt=20.736000, rms=0.561 (0.186%), neg=0, invalid=766 0235: dt=20.736000, rms=0.560 (0.201%), neg=0, invalid=766 0236: dt=20.736000, rms=0.559 (0.226%), neg=0, invalid=766 0237: dt=20.736000, rms=0.558 (0.230%), neg=0, invalid=766 0238: dt=20.736000, rms=0.556 (0.228%), neg=0, invalid=766 0239: dt=20.736000, rms=0.555 (0.216%), neg=0, invalid=766 0240: dt=20.736000, rms=0.554 (0.199%), neg=0, invalid=766 0241: dt=20.736000, rms=0.553 (0.192%), neg=0, invalid=766 0242: dt=20.736000, rms=0.552 (0.199%), neg=0, invalid=766 0243: dt=20.736000, rms=0.551 (0.198%), neg=0, invalid=766 0244: dt=20.736000, rms=0.550 (0.186%), neg=0, invalid=766 0245: dt=20.736000, rms=0.549 (0.175%), neg=0, invalid=766 0246: dt=20.736000, rms=0.548 (0.168%), neg=0, invalid=766 0247: dt=20.736000, rms=0.547 (0.160%), neg=0, invalid=766 0248: dt=20.736000, rms=0.546 (0.158%), neg=0, invalid=766 0249: dt=20.736000, rms=0.545 (0.159%), neg=0, invalid=766 0250: dt=20.736000, rms=0.544 (0.150%), neg=0, invalid=766 0251: dt=20.736000, rms=0.544 (0.138%), neg=0, invalid=766 0252: dt=20.736000, rms=0.543 (0.131%), neg=0, invalid=766 0253: dt=20.736000, rms=0.542 (0.127%), neg=0, invalid=766 0254: dt=20.736000, rms=0.542 (0.119%), neg=0, invalid=766 0255: dt=20.736000, rms=0.541 (0.117%), neg=0, invalid=766 0256: dt=20.736000, rms=0.540 (0.117%), neg=0, invalid=766 0257: dt=20.736000, rms=0.540 (0.109%), neg=0, invalid=766 0258: dt=20.736000, rms=0.539 (0.104%), neg=0, invalid=766 0259: dt=20.736000, rms=0.539 (0.098%), neg=0, invalid=766 0260: dt=20.736000, rms=0.538 (0.095%), neg=0, invalid=766 0261: dt=20.736000, rms=0.538 (0.093%), neg=0, invalid=766 0262: dt=20.736000, rms=0.537 (0.087%), neg=0, invalid=766 0263: dt=20.736000, rms=0.537 (0.081%), neg=0, invalid=766 0264: dt=20.736000, rms=0.536 (0.076%), neg=0, invalid=766 0265: dt=20.736000, rms=0.536 (0.075%), neg=0, invalid=766 0266: dt=20.736000, rms=0.535 (0.074%), neg=0, invalid=766 0267: dt=20.736000, rms=0.535 (0.073%), neg=0, invalid=766 0268: dt=20.736000, rms=0.535 (0.071%), neg=0, invalid=766 0269: dt=20.736000, rms=0.534 (0.067%), neg=0, invalid=766 0270: dt=20.736000, rms=0.534 (0.068%), neg=0, invalid=766 0271: dt=20.736000, rms=0.534 (0.066%), neg=0, invalid=766 0272: dt=20.736000, rms=0.533 (0.063%), neg=0, invalid=766 0273: dt=20.736000, rms=0.533 (0.058%), neg=0, invalid=766 0274: dt=20.736000, rms=0.533 (0.062%), neg=0, invalid=766 0275: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0276: dt=20.736000, rms=0.532 (0.057%), neg=0, invalid=766 0277: dt=20.736000, rms=0.532 (0.059%), neg=0, invalid=766 0278: dt=20.736000, rms=0.531 (0.054%), neg=0, invalid=766 0279: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0280: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0281: dt=20.736000, rms=0.531 (0.045%), neg=0, invalid=766 0282: dt=20.736000, rms=0.530 (0.047%), neg=0, invalid=766 0283: dt=20.736000, rms=0.530 (0.050%), neg=0, invalid=766 0284: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0285: dt=20.736000, rms=0.530 (0.046%), neg=0, invalid=766 0286: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0287: dt=20.736000, rms=0.529 (0.042%), neg=0, invalid=766 0288: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0289: dt=20.736000, rms=0.529 (0.038%), neg=0, invalid=766 0290: dt=20.736000, rms=0.529 (0.037%), neg=0, invalid=766 0291: dt=20.736000, rms=0.528 (0.037%), neg=0, invalid=766 0292: dt=20.736000, rms=0.528 (0.033%), neg=0, invalid=766 0293: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0294: dt=20.736000, rms=0.528 (0.035%), neg=0, invalid=766 0295: dt=20.736000, rms=0.528 (0.036%), neg=0, invalid=766 0296: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0297: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0298: dt=20.736000, rms=0.527 (0.030%), neg=0, invalid=766 0299: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0300: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0301: dt=20.736000, rms=0.527 (0.028%), neg=0, invalid=766 0302: dt=20.736000, rms=0.527 (0.029%), neg=0, invalid=766 0303: dt=20.736000, rms=0.526 (0.031%), neg=0, invalid=766 0304: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0305: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0306: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0307: dt=20.736000, rms=0.526 (0.024%), neg=0, invalid=766 0308: dt=20.736000, rms=0.526 (0.028%), neg=0, invalid=766 0309: dt=20.736000, rms=0.526 (0.027%), neg=0, invalid=766 0310: dt=20.736000, rms=0.526 (0.023%), neg=0, invalid=766 0311: dt=20.736000, rms=0.525 (0.026%), neg=0, invalid=766 0312: dt=20.736000, rms=0.525 (0.022%), neg=0, invalid=766 0313: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0314: dt=20.736000, rms=0.525 (0.024%), neg=0, invalid=766 0315: dt=580.608000, rms=0.525 (0.040%), neg=0, invalid=766 0316: dt=31.104000, rms=0.525 (0.015%), neg=0, invalid=766 0317: dt=31.104000, rms=0.525 (0.007%), neg=0, invalid=766 0318: dt=31.104000, rms=0.525 (0.004%), neg=0, invalid=766 0319: dt=31.104000, rms=0.525 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=766 0320: dt=136.072072, rms=0.523 (0.371%), neg=0, invalid=766 0321: dt=36.288000, rms=0.522 (0.046%), neg=0, invalid=766 0322: dt=36.288000, rms=0.522 (0.054%), neg=0, invalid=766 0323: dt=36.288000, rms=0.522 (0.039%), neg=0, invalid=766 0324: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=766 0325: dt=36.288000, rms=0.522 (0.058%), neg=0, invalid=766 0326: dt=36.288000, rms=0.521 (0.085%), neg=0, invalid=766 0327: dt=36.288000, rms=0.521 (0.066%), neg=0, invalid=766 0328: dt=36.288000, rms=0.521 (0.044%), neg=0, invalid=766 0329: dt=36.288000, rms=0.520 (0.041%), neg=0, invalid=766 0330: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0331: dt=36.288000, rms=0.520 (0.046%), neg=0, invalid=766 0332: dt=36.288000, rms=0.520 (0.048%), neg=0, invalid=766 0333: dt=36.288000, rms=0.519 (0.056%), neg=0, invalid=766 0334: dt=36.288000, rms=0.519 (0.055%), neg=0, invalid=766 0335: dt=36.288000, rms=0.519 (0.053%), neg=0, invalid=766 0336: dt=36.288000, rms=0.518 (0.052%), neg=0, invalid=766 0337: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0338: dt=36.288000, rms=0.518 (0.042%), neg=0, invalid=766 0339: dt=36.288000, rms=0.518 (0.041%), neg=0, invalid=766 0340: dt=36.288000, rms=0.518 (0.047%), neg=0, invalid=766 0341: dt=36.288000, rms=0.517 (0.046%), neg=0, invalid=766 0342: dt=36.288000, rms=0.517 (0.035%), neg=0, invalid=766 0343: dt=36.288000, rms=0.517 (0.036%), neg=0, invalid=766 0344: dt=36.288000, rms=0.517 (0.033%), neg=0, invalid=766 0345: dt=36.288000, rms=0.517 (0.031%), neg=0, invalid=766 0346: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0347: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0348: dt=36.288000, rms=0.516 (0.038%), neg=0, invalid=766 0349: dt=36.288000, rms=0.516 (0.033%), neg=0, invalid=766 0350: dt=36.288000, rms=0.516 (0.034%), neg=0, invalid=766 0351: dt=36.288000, rms=0.516 (0.032%), neg=0, invalid=766 0352: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0353: dt=36.288000, rms=0.515 (0.027%), neg=0, invalid=766 0354: dt=36.288000, rms=0.515 (0.032%), neg=0, invalid=766 0355: dt=36.288000, rms=0.515 (0.036%), neg=0, invalid=766 0356: dt=36.288000, rms=0.515 (0.031%), neg=0, invalid=766 0357: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=766 0358: dt=36.288000, rms=0.515 (0.022%), neg=0, invalid=766 0359: dt=36.288000, rms=0.514 (0.028%), neg=0, invalid=766 0360: dt=36.288000, rms=0.514 (0.026%), neg=0, invalid=766 0361: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0362: dt=36.288000, rms=0.514 (0.025%), neg=0, invalid=766 0363: dt=36.288000, rms=0.514 (0.024%), neg=0, invalid=766 0364: dt=124.416000, rms=0.514 (0.012%), neg=0, invalid=766 0365: dt=124.416000, rms=0.514 (-0.159%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 0366: dt=20.227979, rms=0.525 (0.130%), neg=0, invalid=766 0367: dt=31.326316, rms=0.524 (0.190%), neg=0, invalid=766 0368: dt=12.972973, rms=0.523 (0.137%), neg=0, invalid=766 0369: dt=59.508772, rms=0.522 (0.302%), neg=0, invalid=766 0370: dt=13.479452, rms=0.521 (0.263%), neg=0, invalid=766 0371: dt=179.200000, rms=0.517 (0.721%), neg=0, invalid=766 0372: dt=24.457539, rms=0.514 (0.537%), neg=0, invalid=766 0373: dt=21.157025, rms=0.513 (0.170%), neg=0, invalid=766 0374: dt=38.303030, rms=0.512 (0.170%), neg=0, invalid=766 0375: dt=11.200000, rms=0.512 (0.098%), neg=0, invalid=766 0376: dt=44.800000, rms=0.511 (0.160%), neg=0, invalid=766 0377: dt=11.200000, rms=0.511 (0.082%), neg=0, invalid=766 0378: dt=38.400000, rms=0.510 (0.132%), neg=0, invalid=766 0379: dt=11.200000, rms=0.509 (0.068%), neg=0, invalid=766 0380: dt=25.600000, rms=0.509 (0.079%), neg=0, invalid=766 0381: dt=11.200000, rms=0.509 (0.048%), neg=0, invalid=766 0382: dt=11.200000, rms=0.509 (0.055%), neg=0, invalid=766 0383: dt=11.200000, rms=0.508 (0.066%), neg=0, invalid=766 0384: dt=11.200000, rms=0.508 (0.092%), neg=0, invalid=766 0385: dt=11.200000, rms=0.507 (0.109%), neg=0, invalid=766 0386: dt=11.200000, rms=0.506 (0.139%), neg=0, invalid=766 0387: dt=11.200000, rms=0.506 (0.146%), neg=0, invalid=766 0388: dt=11.200000, rms=0.505 (0.155%), neg=0, invalid=766 0389: dt=11.200000, rms=0.504 (0.151%), neg=0, invalid=766 0390: dt=11.200000, rms=0.503 (0.168%), neg=0, invalid=766 0391: dt=11.200000, rms=0.503 (0.165%), neg=0, invalid=766 0392: dt=11.200000, rms=0.502 (0.158%), neg=0, invalid=766 0393: dt=11.200000, rms=0.501 (0.146%), neg=0, invalid=766 0394: dt=11.200000, rms=0.500 (0.133%), neg=0, invalid=766 0395: dt=11.200000, rms=0.500 (0.140%), neg=0, invalid=766 0396: dt=11.200000, rms=0.499 (0.132%), neg=0, invalid=766 0397: dt=11.200000, rms=0.498 (0.118%), neg=0, invalid=766 0398: dt=11.200000, rms=0.498 (0.112%), neg=0, invalid=766 0399: dt=11.200000, rms=0.497 (0.116%), neg=0, invalid=766 0400: dt=11.200000, rms=0.497 (0.105%), neg=0, invalid=766 0401: dt=11.200000, rms=0.496 (0.097%), neg=0, invalid=766 0402: dt=11.200000, rms=0.496 (0.083%), neg=0, invalid=766 0403: dt=11.200000, rms=0.495 (0.089%), neg=0, invalid=766 0404: dt=11.200000, rms=0.495 (0.084%), neg=0, invalid=766 0405: dt=11.200000, rms=0.495 (0.074%), neg=0, invalid=766 0406: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0407: dt=11.200000, rms=0.494 (0.060%), neg=0, invalid=766 0408: dt=11.200000, rms=0.494 (0.063%), neg=0, invalid=766 0409: dt=11.200000, rms=0.493 (0.054%), neg=0, invalid=766 0410: dt=11.200000, rms=0.493 (0.053%), neg=0, invalid=766 0411: dt=11.200000, rms=0.493 (0.040%), neg=0, invalid=766 0412: dt=11.200000, rms=0.493 (0.051%), neg=0, invalid=766 0413: dt=11.200000, rms=0.493 (0.041%), neg=0, invalid=766 0414: dt=11.200000, rms=0.492 (0.040%), neg=0, invalid=766 0415: dt=11.200000, rms=0.492 (0.035%), neg=0, invalid=766 0416: dt=11.200000, rms=0.492 (0.041%), neg=0, invalid=766 0417: dt=11.200000, rms=0.492 (0.045%), neg=0, invalid=766 0418: dt=11.200000, rms=0.492 (0.031%), neg=0, invalid=766 0419: dt=11.200000, rms=0.491 (0.026%), neg=0, invalid=766 0420: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0421: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=766 0422: dt=11.200000, rms=0.491 (0.023%), neg=0, invalid=766 0423: dt=11.200000, rms=0.491 (0.019%), neg=0, invalid=766 0424: dt=25.600000, rms=0.491 (0.018%), neg=0, invalid=766 0425: dt=25.600000, rms=0.491 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=766 0426: dt=28.444444, rms=0.490 (0.167%), neg=0, invalid=766 0427: dt=12.000000, rms=0.490 (0.084%), neg=0, invalid=766 0428: dt=9.600000, rms=0.489 (0.017%), neg=0, invalid=766 0429: dt=9.600000, rms=0.489 (0.022%), neg=0, invalid=766 0430: dt=9.600000, rms=0.489 (0.014%), neg=0, invalid=766 0431: dt=9.600000, rms=0.489 (0.005%), neg=0, invalid=766 0432: dt=25.600000, rms=0.489 (0.013%), neg=0, invalid=766 0433: dt=4.000000, rms=0.489 (0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0434: dt=0.000000, rms=0.519 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 0435: dt=0.000000, rms=0.519 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=766 0436: dt=1.963333, rms=0.567 (1.560%), neg=0, invalid=766 0437: dt=0.525000, rms=0.567 (0.074%), neg=0, invalid=766 0438: dt=0.448000, rms=0.567 (0.019%), neg=0, invalid=766 0439: dt=0.448000, rms=0.567 (-0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=766 0440: dt=1.282051, rms=0.566 (0.177%), neg=0, invalid=766 0441: dt=0.448000, rms=0.565 (0.014%), neg=0, invalid=766 0442: dt=0.448000, rms=0.565 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 0443: dt=0.448000, rms=0.502 (2.666%), neg=0, invalid=766 0444: dt=0.448000, rms=0.499 (0.609%), neg=0, invalid=766 0445: dt=0.448000, rms=0.497 (0.408%), neg=0, invalid=766 0446: dt=0.448000, rms=0.495 (0.275%), neg=0, invalid=766 0447: dt=0.448000, rms=0.494 (0.209%), neg=0, invalid=766 0448: dt=0.448000, rms=0.493 (0.162%), neg=0, invalid=766 0449: dt=0.028000, rms=0.493 (0.007%), neg=0, invalid=766 0450: dt=0.028000, rms=0.493 (0.009%), neg=0, invalid=766 0451: dt=0.028000, rms=0.493 (0.015%), neg=0, invalid=766 0452: dt=0.028000, rms=0.493 (0.023%), neg=0, invalid=766 0453: dt=0.028000, rms=0.493 (0.028%), neg=0, invalid=766 0454: dt=0.028000, rms=0.493 (0.031%), neg=0, invalid=766 0455: dt=0.028000, rms=0.493 (0.037%), neg=0, invalid=766 0456: dt=0.028000, rms=0.492 (0.038%), neg=0, invalid=766 0457: dt=0.028000, rms=0.492 (0.039%), neg=0, invalid=766 0458: dt=0.028000, rms=0.492 (0.043%), neg=0, invalid=766 0459: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0460: dt=0.028000, rms=0.492 (0.042%), neg=0, invalid=766 0461: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0462: dt=0.028000, rms=0.491 (0.043%), neg=0, invalid=766 0463: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0464: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=766 0465: dt=0.028000, rms=0.491 (0.039%), neg=0, invalid=766 0466: dt=0.028000, rms=0.490 (0.039%), neg=0, invalid=766 0467: dt=0.028000, rms=0.490 (0.036%), neg=0, invalid=766 0468: dt=0.028000, rms=0.490 (0.002%), neg=0, invalid=766 0469: dt=0.028000, rms=0.490 (0.004%), neg=0, invalid=766 0470: dt=0.028000, rms=0.490 (0.006%), neg=0, invalid=766 0471: dt=0.028000, rms=0.490 (0.008%), neg=0, invalid=766 0472: dt=0.028000, rms=0.490 (0.007%), neg=0, invalid=766 0473: dt=0.461538, rms=0.490 (0.033%), neg=0, invalid=766 0474: dt=0.024000, rms=0.490 (0.001%), neg=0, invalid=766 0475: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0476: dt=0.024000, rms=0.490 (0.003%), neg=0, invalid=766 0477: dt=0.024000, rms=0.490 (0.004%), neg=0, invalid=766 0478: dt=0.024000, rms=0.490 (0.005%), neg=0, invalid=766 0479: dt=0.024000, rms=0.490 (0.006%), neg=0, invalid=766 0480: dt=0.024000, rms=0.490 (0.007%), neg=0, invalid=766 0481: dt=0.024000, rms=0.490 (0.008%), neg=0, invalid=766 0482: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0483: dt=0.024000, rms=0.490 (0.009%), neg=0, invalid=766 0484: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0485: dt=0.024000, rms=0.490 (0.010%), neg=0, invalid=766 0486: dt=0.024000, rms=0.490 (0.011%), neg=0, invalid=766 0487: dt=0.024000, rms=0.489 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=766 0488: dt=0.384000, rms=0.486 (0.728%), neg=0, invalid=766 0489: dt=0.028000, rms=0.486 (0.009%), neg=0, invalid=766 0490: dt=0.028000, rms=0.486 (0.010%), neg=0, invalid=766 0491: dt=0.028000, rms=0.486 (0.017%), neg=0, invalid=766 0492: dt=0.028000, rms=0.486 (0.024%), neg=0, invalid=766 0493: dt=0.028000, rms=0.485 (0.027%), neg=0, invalid=766 0494: dt=0.028000, rms=0.485 (0.030%), neg=0, invalid=766 0495: dt=0.028000, rms=0.485 (0.029%), neg=0, invalid=766 0496: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=766 0497: dt=0.028000, rms=0.485 (0.026%), neg=0, invalid=766 0498: dt=0.028000, rms=0.485 (0.024%), neg=0, invalid=766 0499: dt=0.028000, rms=0.485 (0.018%), neg=0, invalid=766 0500: dt=0.000000, rms=0.485 (-0.001%), neg=0, invalid=766 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... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 0501: dt=73.984000, rms=0.483 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=766 0502: dt=129.472000, rms=0.482 (0.113%), neg=0, invalid=766 0503: dt=221.952000, rms=0.482 (0.068%), neg=0, invalid=766 0504: dt=129.472000, rms=0.481 (0.056%), neg=0, invalid=766 0505: dt=110.976000, rms=0.481 (0.027%), neg=0, invalid=766 0506: dt=110.976000, rms=0.481 (0.030%), neg=0, invalid=766 0507: dt=110.976000, rms=0.481 (0.041%), neg=0, invalid=766 0508: dt=110.976000, rms=0.481 (0.053%), neg=0, invalid=766 0509: dt=110.976000, rms=0.481 (0.049%), neg=0, invalid=766 0510: dt=110.976000, rms=0.480 (0.059%), neg=0, invalid=766 0511: dt=110.976000, rms=0.480 (0.053%), neg=0, invalid=766 0512: dt=110.976000, rms=0.480 (0.054%), neg=0, invalid=766 0513: dt=110.976000, rms=0.480 (0.049%), neg=0, invalid=766 0514: dt=110.976000, rms=0.479 (0.049%), neg=0, invalid=766 0515: dt=110.976000, rms=0.479 (0.047%), neg=0, invalid=766 0516: dt=110.976000, rms=0.479 (0.044%), neg=0, invalid=766 0517: dt=110.976000, rms=0.479 (0.043%), neg=0, invalid=766 0518: dt=110.976000, rms=0.478 (0.037%), neg=0, invalid=766 0519: dt=110.976000, rms=0.478 (0.036%), neg=0, invalid=766 0520: dt=110.976000, rms=0.478 (0.031%), neg=0, invalid=766 0521: dt=110.976000, rms=0.478 (0.030%), neg=0, invalid=766 0522: dt=110.976000, rms=0.478 (0.028%), neg=0, invalid=766 0523: dt=110.976000, rms=0.478 (0.025%), neg=0, invalid=766 0524: dt=110.976000, rms=0.478 (0.022%), neg=0, invalid=766 0525: dt=443.904000, rms=0.478 (0.005%), neg=0, invalid=766 0526: dt=443.904000, rms=0.478 (-0.062%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 0527: dt=38.588235, rms=0.477 (0.078%), neg=0, invalid=766 0528: dt=103.680000, rms=0.477 (0.118%), neg=0, invalid=766 0529: dt=145.152000, rms=0.475 (0.331%), neg=0, invalid=766 0530: dt=36.288000, rms=0.475 (0.018%), neg=0, invalid=766 0531: dt=36.288000, rms=0.475 (0.035%), neg=0, invalid=766 0532: dt=36.288000, rms=0.475 (0.064%), neg=0, invalid=766 0533: dt=36.288000, rms=0.474 (0.087%), neg=0, invalid=766 0534: dt=36.288000, rms=0.474 (0.100%), neg=0, invalid=766 0535: dt=18.144000, rms=0.474 (0.019%), neg=0, invalid=766 0536: dt=9.072000, rms=0.474 (0.010%), neg=0, invalid=766 0537: dt=6.480000, rms=0.474 (0.007%), neg=0, invalid=766 0538: dt=0.101250, rms=0.474 (0.000%), neg=0, invalid=766 0539: dt=0.025312, rms=0.474 (0.000%), neg=0, invalid=766 0540: dt=0.012656, rms=0.474 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 0541: dt=132.512821, rms=0.471 (0.546%), neg=0, invalid=766 0542: dt=44.800000, rms=0.470 (0.141%), neg=0, invalid=766 0543: dt=103.680000, rms=0.470 (0.116%), neg=0, invalid=766 0544: dt=414.720000, rms=0.468 (0.287%), neg=0, invalid=766 0545: dt=43.000000, rms=0.468 (0.096%), neg=0, invalid=766 0546: dt=36.288000, rms=0.468 (0.019%), neg=0, invalid=766 0547: dt=36.288000, rms=0.468 (0.017%), neg=0, invalid=766 0548: dt=18.144000, rms=0.468 (0.008%), neg=0, invalid=766 0549: dt=9.072000, rms=0.468 (0.004%), neg=0, invalid=766 0550: dt=9.072000, rms=0.468 (0.005%), neg=0, invalid=766 0551: dt=0.567000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 0552: dt=11.200000, rms=0.467 (0.281%), neg=0, invalid=766 0553: dt=0.700000, rms=0.467 (0.016%), neg=0, invalid=766 0554: dt=0.350000, rms=0.467 (0.008%), neg=0, invalid=766 0555: dt=0.175000, rms=0.467 (0.004%), neg=0, invalid=766 0556: dt=0.021875, rms=0.467 (0.000%), neg=0, invalid=766 0557: dt=0.000684, rms=0.467 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0558: dt=44.800000, rms=0.462 (1.098%), neg=0, invalid=766 0559: dt=44.800000, rms=0.459 (0.606%), neg=0, invalid=766 0560: dt=38.400000, rms=0.457 (0.489%), neg=0, invalid=766 0561: dt=44.800000, rms=0.456 (0.222%), neg=0, invalid=766 0562: dt=11.200000, rms=0.455 (0.147%), neg=0, invalid=766 0563: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0564: dt=0.175000, rms=0.455 (0.002%), neg=0, invalid=766 0565: dt=0.043750, rms=0.455 (0.000%), neg=0, invalid=766 0566: dt=0.005469, rms=0.455 (0.000%), neg=0, invalid=766 0567: dt=0.000684, rms=0.455 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0568: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 0569: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 0570: dt=0.906250, rms=0.465 (0.232%), neg=0, invalid=766 0571: dt=0.448000, rms=0.464 (0.065%), neg=0, invalid=766 0572: dt=0.681818, rms=0.464 (0.070%), neg=0, invalid=766 0573: dt=1.792000, rms=0.464 (0.057%), neg=0, invalid=766 0574: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 0575: dt=0.100000, rms=0.464 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0576: dt=1.536000, rms=0.463 (0.243%), neg=0, invalid=766 0577: dt=0.541667, rms=0.462 (0.043%), neg=0, invalid=766 0578: dt=0.541667, rms=0.462 (0.036%), neg=0, invalid=766 0579: dt=0.541667, rms=0.462 (0.056%), neg=0, invalid=766 0580: dt=0.541667, rms=0.462 (0.018%), neg=0, invalid=766 0581: dt=0.541667, rms=0.462 (0.027%), neg=0, invalid=766 0582: dt=0.541667, rms=0.462 (0.024%), neg=0, invalid=766 0583: dt=0.541667, rms=0.462 (0.010%), neg=0, invalid=766 0584: dt=0.000000, rms=0.462 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 0585: dt=0.140550, rms=0.451 (0.763%), neg=0, invalid=766 0586: dt=0.122596, rms=0.449 (0.477%), neg=0, invalid=766 0587: dt=0.112257, rms=0.448 (0.334%), neg=0, invalid=766 0588: dt=0.112000, rms=0.447 (0.265%), neg=0, invalid=766 0589: dt=0.112000, rms=0.446 (0.214%), neg=0, invalid=766 0590: dt=0.112000, rms=0.445 (0.174%), neg=0, invalid=766 0591: dt=0.112000, rms=0.444 (0.144%), neg=0, invalid=766 0592: dt=0.112000, rms=0.444 (0.120%), neg=0, invalid=766 0593: dt=0.112000, rms=0.443 (0.101%), neg=0, invalid=766 0594: dt=0.112000, rms=0.443 (0.086%), neg=0, invalid=766 0595: dt=0.112000, rms=0.442 (0.074%), neg=0, invalid=766 0596: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0597: dt=0.028000, rms=0.442 (0.016%), neg=0, invalid=766 0598: dt=0.028000, rms=0.442 (0.029%), neg=0, invalid=766 0599: dt=0.028000, rms=0.442 (0.040%), neg=0, invalid=766 0600: dt=0.028000, rms=0.442 (0.049%), neg=0, invalid=766 0601: dt=0.028000, rms=0.442 (0.011%), neg=0, invalid=766 0602: dt=0.028000, rms=0.442 (0.021%), neg=0, invalid=766 0603: dt=0.028000, rms=0.442 (0.030%), neg=0, invalid=766 0604: dt=0.028000, rms=0.441 (0.037%), neg=0, invalid=766 0605: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0606: dt=0.028000, rms=0.441 (0.045%), neg=0, invalid=766 0607: dt=0.028000, rms=0.441 (0.007%), neg=0, invalid=766 0608: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0609: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0610: dt=0.112000, rms=0.441 (0.025%), neg=0, invalid=766 0611: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0612: dt=0.028000, rms=0.441 (0.006%), neg=0, invalid=766 0613: dt=0.028000, rms=0.441 (0.011%), neg=0, invalid=766 0614: dt=0.028000, rms=0.441 (0.015%), neg=0, invalid=766 0615: dt=0.028000, rms=0.441 (0.018%), neg=0, invalid=766 0616: dt=0.028000, rms=0.440 (0.021%), neg=0, invalid=766 0617: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 0618: dt=0.028000, rms=0.440 (0.008%), neg=0, invalid=766 0619: dt=0.028000, rms=0.440 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=766 0620: dt=0.028000, rms=0.440 (0.058%), neg=0, invalid=766 0621: dt=0.028000, rms=0.440 (0.054%), neg=0, invalid=766 0622: dt=0.024000, rms=0.440 (0.043%), neg=0, invalid=766 0623: dt=0.024000, rms=0.439 (0.041%), neg=0, invalid=766 0624: dt=0.024000, rms=0.439 (0.075%), neg=0, invalid=766 0625: dt=0.024000, rms=0.439 (0.035%), neg=0, invalid=766 0626: dt=0.024000, rms=0.439 (0.064%), neg=0, invalid=766 0627: dt=0.024000, rms=0.438 (0.086%), neg=0, invalid=766 0628: dt=0.024000, rms=0.438 (0.101%), neg=0, invalid=766 0629: dt=0.024000, rms=0.437 (0.108%), neg=0, invalid=766 0630: dt=0.024000, rms=0.437 (0.109%), neg=0, invalid=766 0631: dt=0.024000, rms=0.436 (0.104%), neg=0, invalid=766 0632: dt=0.024000, rms=0.436 (0.095%), neg=0, invalid=766 0633: dt=0.024000, rms=0.436 (0.082%), neg=0, invalid=766 0634: dt=0.024000, rms=0.435 (0.068%), neg=0, invalid=766 0635: dt=0.024000, rms=0.435 (0.053%), neg=0, invalid=766 0636: dt=0.024000, rms=0.435 (0.038%), neg=0, invalid=766 0637: dt=0.024000, rms=0.435 (0.023%), neg=0, invalid=766 0638: dt=0.024000, rms=0.435 (0.009%), neg=0, invalid=766 0639: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 4 hours, 9 minutes and 13 seconds. #-------------------------------------- #@# CA Reg Inv Wed Mar 3 20:50:02 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Mar 3 20:51:02 CET 2010
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/home/kutato/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11104963 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA Wed Mar 3 20:52:16 CET 2010
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.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 '/home/kutato/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (45, 52, 28) --> (207, 202, 237) using (99, 102, 133) as brain centroid... mean wm in atlas = 126, using box (79,84,107) --> (118, 120,158) to find MRI wm before smoothing, mri peak at 141 after smoothing, mri peak at 140, scaling input intensities by 0.900 scaling channel 0 by 0.9
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-17103.0 (thresh=-17085.9) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-14667.9, old_max_log_p =-14667.9 (thresh=-14653.3) 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 2 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14488.4, old_max_log_p =-14667.9 (thresh=-14653.3) 1.036 -0.063 -0.081 14.725; 0.070 1.213 0.222 -79.106; 0.083 -0.208 0.964 -0.991; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14488.4 (thresh=-14473.9) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-14436.8, old_max_log_p =-14436.8 (thresh=-14422.4) 1.020 -0.062 -0.080 16.460; 0.069 1.216 0.206 -77.328; 0.085 -0.191 0.982 -5.976; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14436.8 (thresh=-14422.4) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-14336.6, old_max_log_p =-14336.6 (thresh=-14322.3) 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 3481 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 14336.6 tol 0.000010 Resulting transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -14336.6 (old=-17103.0) transform before final EM align: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 382743 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02415 -0.06237 -0.07994 15.55589; 0.06906 1.22541 0.20788 -77.96246; 0.08461 -0.19002 0.97860 -5.07645; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 1833208.1 tol 0.000000 final transform: 1.024 -0.062 -0.080 15.556; 0.069 1.225 0.208 -77.962; 0.085 -0.190 0.979 -5.076; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta... registration took 49 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Wed Mar 3 21:42:15 CET 2010
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
$Id: mri_seg_diff.c,v 1.3.2.1 2008/09/03 22:02:00 nicks Exp $ cwd /home/kutato/freesurfer/subjects/C1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname localhost.localdomain machine x86_64 user kutato Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmenations No difference found.
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/kutato/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /home/kutato/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /home/kutato/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, overlap=0.688) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (4597 voxels, peak = 32), gca=32.4 gca peak = 0.14982 (20) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, overlap=0.231) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (4889 voxels, peak = 28), gca=28.5 gca peak = 0.28003 (97) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (501 voxels, peak = 102), gca=101.8 gca peak = 0.18160 (96) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, overlap=0.407) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (486 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1299 voxels, peak = 78), gca=77.5 gca peak = 0.32745 (63) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1344 voxels, peak = 77), gca=77.2 gca peak = 0.08597 (105) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41820 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (46122 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, overlap=0.045) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (75062 voxels, peak = 80), gca=80.3 gca peak = 0.08598 (64) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, overlap=0.074) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (76201 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1246 voxels, peak = 85), gca=85.2 gca peak = 0.18227 (75) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, overlap=0.228) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1215 voxels, peak = 84), gca=84.4 gca peak = 0.10629 (62) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (27928 voxels, peak = 85), gca=85.2 gca peak = 0.11668 (59) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (27962 voxels, peak = 83), gca=82.6 gca peak = 0.17849 (88) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.27 x + 0.0 (5904 voxels, peak = 112), gca=112.2 gca peak = 0.16819 (86) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 1.25 x + 0.0 (5909 voxels, peak = 108), gca=107.5 gca peak = 0.41688 (64) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (410 voxels, peak = 80), gca=80.0 gca peak = 0.42394 (62) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (475 voxels, peak = 81), gca=80.6 gca peak = 0.10041 (96) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, overlap=0.774) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5076 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, overlap=0.443) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5043 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, overlap=0.331) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2422 voxels, peak = 91), gca=91.1 gca peak = 0.09624 (82) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, overlap=0.394) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2375 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, overlap=0.000) Brain_Stem (16): linear fit = 1.17 x + 0.0 (12933 voxels, peak = 103), gca=103.4 gca peak = 0.12757 (95) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1711 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, overlap=0.525) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1763 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, overlap=0.902) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (196 voxels, peak = 32), gca=32.4 gca peak = 0.26069 (23) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, overlap=0.240) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (428 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.23 x + 0.0 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14396 (33) mri peak = 0.13979 (32) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, overlap=0.871) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (4597 voxels, peak = 31), gca=31.4 gca peak = 0.13467 (29) mri peak = 0.17627 (32) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, overlap=0.673) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (4889 voxels, peak = 31), gca=31.2 gca peak = 0.27948 (102) mri peak = 0.14881 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (501 voxels, peak = 102), gca=102.0 gca peak = 0.18507 (101) mri peak = 0.17026 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (486 voxels, peak = 101), gca=101.0 gca peak = 0.21463 (78) mri peak = 0.10375 (79) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1299 voxels, peak = 76), gca=76.1 gca peak = 0.27122 (77) mri peak = 0.09830 (81) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1344 voxels, peak = 77), gca=77.0 gca peak = 0.08007 (112) mri peak = 0.07406 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, overlap=0.810) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41820 voxels, peak = 112), gca=112.0 gca peak = 0.08789 (111) mri peak = 0.06674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, overlap=0.795) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (46122 voxels, peak = 114), gca=113.8 gca peak = 0.06240 (80) mri peak = 0.02920 (80) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, overlap=0.591) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (75062 voxels, peak = 78), gca=78.0 gca peak = 0.07094 (77) mri peak = 0.02989 (78) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, overlap=0.711) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (76201 voxels, peak = 75), gca=75.1 gca peak = 0.23769 (85) mri peak = 0.19383 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1246 voxels, peak = 85), gca=85.0 gca peak = 0.13104 (84) mri peak = 0.20311 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, overlap=0.845) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1215 voxels, peak = 86), gca=86.1 gca peak = 0.08141 (85) mri peak = 0.03222 (77) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, overlap=0.690) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (27928 voxels, peak = 83), gca=82.9 gca peak = 0.09212 (83) mri peak = 0.03336 (77) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, overlap=0.736) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27962 voxels, peak = 83), gca=83.0 gca peak = 0.14004 (112) mri peak = 0.10217 (112) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, overlap=0.965) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5904 voxels, peak = 112), gca=112.0 gca peak = 0.13912 (108) mri peak = 0.09415 (109) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5909 voxels, peak = 108), gca=108.0 gca peak = 0.30905 (79) mri peak = 0.18355 (81) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 81), gca=81.0 gca peak = 0.37870 (81) mri peak = 0.20700 (79) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (475 voxels, peak = 79), gca=79.0 gca peak = 0.10116 (99) mri peak = 0.09092 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, overlap=0.963) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5076 voxels, peak = 99), gca=99.0 gca peak = 0.09774 (97) mri peak = 0.09326 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, overlap=0.918) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5043 voxels, peak = 97), gca=97.0 gca peak = 0.08941 (98) mri peak = 0.10672 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2422 voxels, peak = 98), gca=98.0 gca peak = 0.08263 (85) mri peak = 0.10969 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, overlap=0.828) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2375 voxels, peak = 85), gca=85.0 gca peak = 0.06255 (104) mri peak = 0.09760 (101) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, overlap=0.638) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12933 voxels, peak = 104), gca=104.0 gca peak = 0.14189 (104) mri peak = 0.10577 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, overlap=0.808) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, peak = 104), gca=104.0 gca peak = 0.16147 (99) mri peak = 0.09104 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1763 voxels, peak = 99), gca=99.0 gca peak = 0.22647 (34) mri peak = 0.16148 (30) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, overlap=0.851) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (196 voxels, peak = 33), gca=33.2 gca peak = 0.16050 (32) mri peak = 0.14139 (32) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, overlap=0.781) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (428 voxels, peak = 32), gca=32.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26758 (43) gca peak CSF = 0.17739 (47) gca peak Left_Accumbens_area = 0.36131 (79) gca peak Left_undetermined = 0.95107 (38) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.22906 (40) gca peak Right_Accumbens_area = 0.27742 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.12959 (48) gca peak Fifth_Ventricle = 0.50102 (51) gca peak WM_hypointensities = 0.15008 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34132 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 33062 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 306 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77084 changed. image ll: -2.213, PF=1.000 pass 2: 12120 changed. image ll: -2.211, PF=1.000 pass 3: 4101 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 30 minutes and 38 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz C1
reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /home/kutato/freesurfer/subjects/C1/mri/aseg.auto_noCCseg.mgz reading norm from /home/kutato/freesurfer/subjects/C1/mri/norm.mgz 44494 voxels in left wm, 85128 in right wm, xrange [115, 131] global minimum found at slice 125.0, rotations (-3.75, -0.25) final transformation (x=125.0, yr=-3.750, zr=-0.250): 0.998 0.004 -0.065 11.082; -0.004 1.000 0.000 0.509; 0.065 0.000 0.998 -7.901; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 133 113 eigenvectors: -0.002 -0.003 1.000; -0.035 -0.999 -0.003; 0.999 -0.035 0.002; error in mid anterior detected - correcting... writing aseg with callosum to to /home/kutato/freesurfer/subjects/C1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.8 minutes #-------------------------------------- #@# Merge ASeg Wed Mar 3 22:14:45 CET 2010
cp aseg.auto.mgz aseg.mgz
#-------------------------------------------- #@# Intensity Normalization2 Wed Mar 3 22:14:45 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_normalize -f /home/kutato/freesurfer/subjects/C1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using control points from file /home/kutato/freesurfer/subjects/C1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 710 control points... only using 710 control points from file... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 223389 control points removed building Voronoi diagram... performing soap bubble smoothing... 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 brain.mgz 3D bias adjustment took 6 minutes and 6 seconds. using MR volume brainmask.mgz to mask input volume... using wm (255) threshold 245.0 for removing exterior voxels white matter peak found at 111 gm peak at 77 (77), valley at 40 (40) csf peak at 28, setting threshold to 60 white matter peak found at 111 gm peak at 78 (78), valley at 40 (40) csf peak at 29, setting threshold to 61 #-------------------------------------------- #@# Mask BFS Wed Mar 3 22:20:55 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Mar 3 22:20:58 CET 2010
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (109.0): 107.5 +- 7.5 [80.0 --> 125.0] GM (68.0) : 65.0 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10488 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4151 filled 110391 bright non-wm voxels segmented. 7168 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz...
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume... auto filling took 0.76 minutes reading wm segmentation from wm.seg.mgz... 404 voxels added to wm to prevent paths from MTL structures to cortex 6112 additional wm voxels added 0 additional wm voxels added SEG EDIT: 68648 voxels turned on, 46182 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 90 new 90 115,126,128 old 90 new 90 writing edited volume to wm.asegedit.mgz....
mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1 pass 1 (xy+): 154 found - 154 modified | TOTAL: 154 pass 2 (xy+): 0 found - 154 modified | TOTAL: 154 pass 1 (xy-): 134 found - 134 modified | TOTAL: 288 pass 2 (xy-): 0 found - 134 modified | TOTAL: 288 pass 1 (yz+): 124 found - 124 modified | TOTAL: 412 pass 2 (yz+): 0 found - 124 modified | TOTAL: 412 pass 1 (yz-): 99 found - 99 modified | TOTAL: 511 pass 2 (yz-): 0 found - 99 modified | TOTAL: 511 pass 1 (xz+): 137 found - 137 modified | TOTAL: 648 pass 2 (xz+): 0 found - 137 modified | TOTAL: 648 pass 1 (xz-): 124 found - 124 modified | TOTAL: 772 pass 2 (xz-): 0 found - 124 modified | TOTAL: 772 Iteration Number : 1 pass 1 (+++): 100 found - 100 modified | TOTAL: 100 pass 2 (+++): 0 found - 100 modified | TOTAL: 100 pass 1 (+++): 97 found - 97 modified | TOTAL: 197 pass 2 (+++): 0 found - 97 modified | TOTAL: 197 pass 1 (+++): 84 found - 84 modified | TOTAL: 281 pass 2 (+++): 0 found - 84 modified | TOTAL: 281 pass 1 (+++): 135 found - 135 modified | TOTAL: 416 pass 2 (+++): 0 found - 135 modified | TOTAL: 416 Iteration Number : 1 pass 1 (++): 141 found - 141 modified | TOTAL: 141 pass 2 (++): 0 found - 141 modified | TOTAL: 141 pass 1 (+-): 205 found - 205 modified | TOTAL: 346 pass 2 (+-): 0 found - 205 modified | TOTAL: 346 pass 1 (--): 152 found - 152 modified | TOTAL: 498 pass 2 (--): 1 found - 153 modified | TOTAL: 499 pass 3 (--): 0 found - 153 modified | TOTAL: 499 pass 1 (-+): 183 found - 183 modified | TOTAL: 682 pass 2 (-+): 0 found - 183 modified | TOTAL: 682 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 23 found - 23 modified | TOTAL: 45 pass 2 (xy-): 0 found - 23 modified | TOTAL: 45 pass 1 (yz+): 19 found - 19 modified | TOTAL: 64 pass 2 (yz+): 0 found - 19 modified | TOTAL: 64 pass 1 (yz-): 37 found - 37 modified | TOTAL: 101 pass 2 (yz-): 0 found - 37 modified | TOTAL: 101 pass 1 (xz+): 39 found - 39 modified | TOTAL: 140 pass 2 (xz+): 0 found - 39 modified | TOTAL: 140 pass 1 (xz-): 22 found - 22 modified | TOTAL: 162 pass 2 (xz-): 0 found - 22 modified | TOTAL: 162 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 pass 1 (+++): 4 found - 4 modified | TOTAL: 19 pass 2 (+++): 0 found - 4 modified | TOTAL: 19 Iteration Number : 2 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 22 found - 22 modified | TOTAL: 35 pass 2 (+-): 0 found - 22 modified | TOTAL: 35 pass 1 (--): 17 found - 17 modified | TOTAL: 52 pass 2 (--): 0 found - 17 modified | TOTAL: 52 pass 1 (-+): 10 found - 10 modified | TOTAL: 62 pass 2 (-+): 0 found - 10 modified | TOTAL: 62 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 1 found - 1 modified | TOTAL: 14 pass 2 (xz-): 0 found - 1 modified | TOTAL: 14 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 2131 (out of 674704: 0.315842) keeping edits binarizing input wm segmentation... Ambiguous edge configurations...
Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels
mri_pretess done
#-------------------------------------------- #@# Fill Wed Mar 3 22:23:31 CET 2010 /home/kutato/freesurfer/subjects/C1/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.056 -0.008 -0.055 1.601; 0.015 1.203 0.189 -64.936; 0.065 -0.169 0.971 -3.018; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 619 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 119, 151), TAL = (2.0, 23.0, 9.0) talairach voxel to voxel transform 0.943 0.014 0.050 -0.471; -0.002 0.809 -0.158 52.074; -0.063 0.140 0.999 12.198; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 119, 151) --> (2.0, 23.0, 9.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 23.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 9.00) SRC: (110.64, 124.32, 172.81) search lh wm seed point around talairach space (-16.00, 23.00, 9.00), SRC: (144.61, 124.24, 170.53) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Mar 3 22:24:28 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 12 found - 12 modified | TOTAL: 25 pass 2 (xy-): 0 found - 12 modified | TOTAL: 25 pass 1 (yz+): 10 found - 10 modified | TOTAL: 35 pass 2 (yz+): 0 found - 10 modified | TOTAL: 35 pass 1 (yz-): 22 found - 22 modified | TOTAL: 57 pass 2 (yz-): 0 found - 22 modified | TOTAL: 57 pass 1 (xz+): 15 found - 15 modified | TOTAL: 72 pass 2 (xz+): 0 found - 15 modified | TOTAL: 72 pass 1 (xz-): 5 found - 5 modified | TOTAL: 77 pass 2 (xz-): 0 found - 5 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 9 found - 9 modified | TOTAL: 15 pass 2 (+-): 0 found - 9 modified | TOTAL: 15 pass 1 (--): 13 found - 13 modified | TOTAL: 28 pass 2 (--): 0 found - 13 modified | TOTAL: 28 pass 1 (-+): 3 found - 3 modified | TOTAL: 31 pass 2 (-+): 0 found - 3 modified | TOTAL: 31 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 128 (out of 320366: 0.039954) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ slice 50: 715 vertices, 806 faces slice 60: 6587 vertices, 6870 faces slice 70: 16362 vertices, 16829 faces slice 80: 27996 vertices, 28461 faces slice 90: 40299 vertices, 40842 faces slice 100: 52688 vertices, 53229 faces slice 110: 65001 vertices, 65581 faces slice 120: 77662 vertices, 78249 faces slice 130: 89134 vertices, 89714 faces slice 140: 100712 vertices, 101362 faces slice 150: 112906 vertices, 113608 faces slice 160: 123188 vertices, 123863 faces slice 170: 130916 vertices, 131557 faces slice 180: 137022 vertices, 137584 faces slice 190: 141777 vertices, 142325 faces slice 200: 145789 vertices, 146310 faces slice 210: 149464 vertices, 149996 faces slice 220: 152836 vertices, 153278 faces slice 230: 152952 vertices, 153360 faces slice 240: 152952 vertices, 153360 faces slice 250: 152952 vertices, 153360 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components... 152952 voxel in cpt #1: X=-408 [v=152952,e=460080,f=306720] located at (-25.554226, -6.675813, -2.117488) For the whole surface: X=-408 [v=152952,e=460080,f=306720] One single component has been found nothing to do done
#-------------------------------------------- #@# Smooth1 lh Wed Mar 3 22:24:41 CET 2010
mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/kutato/freesurfer/subjects/C1/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Mar 3 22:24:46 CET 2010
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/kutato/freesurfer/subjects/C1/scripts avg radius = 49.0 mm, total surface area = 79501 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.071 (target=0.015) step 030: RMS=0.069 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.065 (target=0.015) step 045: RMS=0.065 (target=0.015) step 050: RMS=0.065 (target=0.015) step 055: RMS=0.065 (target=0.015) step 060: RMS=0.065 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Mar 3 22:25:42 CET 2010 /home/kutato/freesurfer/subjects/C1/scripts
mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, sigma=0.0, host=local, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90
surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.88 (0.00-->27.18) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-1.82-->2.32) tol=1.0e-01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
301: dt: 15.53, sse: 8540.7 (0.052, 34.9, 0.000), neg: 26636 (%4.389:%4.53), avgs: 32 302: dt: 0.29, sse: 8539.7 (0.052, 34.9, 0.000), neg: 26636 (%4.375:%4.52), avgs: 32 303: dt: 0.29, sse: 8538.0 (0.052, 34.9, 0.000), neg: 26627 (%4.349:%4.52), avgs: 32 304: dt: 0.29, sse: 8536.1 (0.052, 34.9, 0.000), neg: 26615 (%4.318:%4.51), avgs: 32 305: dt: 0.29, sse: 8533.4 (0.052, 34.9, 0.000), neg: 26609 (%4.275:%4.50), avgs: 32 306: dt: 0.29, sse: 8530.6 (0.052, 34.8, 0.000), neg: 26596 (%4.228:%4.49), avgs: 32 307: dt: 0.29, sse: 8527.6 (0.052, 34.8, 0.000), neg: 26579 (%4.176:%4.48), avgs: 32 308: dt: 0.29, sse: 8524.4 (0.052, 34.8, 0.000), neg: 26560 (%4.119:%4.46), avgs: 32 309: dt: 0.29, sse: 8520.9 (0.052, 34.8, 0.000), neg: 26543 (%4.058:%4.45), avgs: 32 310: dt: 0.29, sse: 8517.4 (0.051, 34.8, 0.000), neg: 26523 (%3.994:%4.43), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->25.82) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.93-->2.40) 311: dt: 0.29, sse: 8514.0 (0.051, 34.8, 0.000), neg: 26509 (%3.932:%4.41), avgs: 32 312: dt: 48.14, sse: 8479.7 (0.051, 34.6, 0.000), neg: 26094 (%3.212:%4.03), avgs: 32 vertex spacing 0.98 +- 0.88 (0.00-->24.45) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.71-->2.54) 313: dt: 3.56, sse: 8469.9 (0.051, 34.7, 0.000), neg: 26269 (%2.998:%4.03), avgs: 8 314: dt: 0.15, sse: 8469.3 (0.051, 34.7, 0.000), neg: 26242 (%2.986:%4.01), avgs: 8 315: dt: 0.15, sse: 8468.6 (0.051, 34.7, 0.000), neg: 26253 (%2.969:%4.00), avgs: 8 316: dt: 0.15, sse: 8467.1 (0.051, 34.7, 0.000), neg: 26267 (%2.942:%3.99), avgs: 8 317: dt: 0.15, sse: 8466.2 (0.051, 34.7, 0.000), neg: 26292 (%2.922:%3.98), avgs: 8 318: dt: 0.15, sse: 8465.3 (0.051, 34.7, 0.000), neg: 26295 (%2.901:%3.97), avgs: 8 319: dt: 0.15, sse: 8465.2 (0.051, 34.7, 0.000), neg: 26300 (%2.890:%3.96), avgs: 8 320: dt: 0.15, sse: 8464.7 (0.051, 34.7, 0.000), neg: 26310 (%2.872:%3.95), avgs: 8 vertex spacing 0.98 +- 0.88 (0.00-->23.63) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.52-->2.61) 321: dt: 0.15, sse: 8464.2 (0.051, 34.7, 0.000), neg: 26327 (%2.854:%3.94), avgs: 8 322: dt: 0.15, sse: 8463.7 (0.051, 34.7, 0.000), neg: 26343 (%2.835:%3.93), avgs: 8 323: dt: 0.15, sse: 8462.9 (0.051, 34.7, 0.000), neg: 26359 (%2.810:%3.93), avgs: 8 324: dt: 2.69, sse: 8458.0 (0.051, 34.7, 0.000), neg: 26415 (%2.703:%3.92), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->23.23) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.47-->2.64) 325: dt: 1.44, sse: 8454.2 (0.051, 34.7, 0.000), neg: 26661 (%2.601:%3.93), avgs: 2 326: dt: 0.09, sse: 8453.8 (0.051, 34.7, 0.000), neg: 26697 (%2.581:%3.93), avgs: 2 327: dt: 0.09, sse: 8452.8 (0.051, 34.8, 0.000), neg: 26737 (%2.553:%3.93), avgs: 2 328: dt: 0.09, sse: 8451.9 (0.051, 34.8, 0.000), neg: 26779 (%2.526:%3.92), avgs: 2 329: dt: 0.09, sse: 8451.5 (0.051, 34.8, 0.000), neg: 26818 (%2.503:%3.92), avgs: 2 330: dt: 0.09, sse: 8450.9 (0.051, 34.8, 0.000), neg: 26880 (%2.480:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.65) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.26-->2.69) 331: dt: 0.09, sse: 8450.2 (0.051, 34.8, 0.000), neg: 26944 (%2.455:%3.91), avgs: 2 332: dt: 0.09, sse: 8449.5 (0.051, 34.8, 0.000), neg: 27007 (%2.430:%3.92), avgs: 2 333: dt: 0.09, sse: 8449.1 (0.051, 34.8, 0.000), neg: 27074 (%2.410:%3.91), avgs: 2 334: dt: 0.09, sse: 8448.9 (0.051, 34.9, 0.000), neg: 27156 (%2.391:%3.92), avgs: 2 335: dt: 0.09, sse: 8448.2 (0.051, 34.9, 0.000), neg: 27231 (%2.368:%3.92), avgs: 2 336: dt: 0.06, sse: 8448.1 (0.051, 34.9, 0.000), neg: 27244 (%2.366:%3.92), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.33) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.39-->2.72) 337: dt: 0.16, sse: 8447.2 (0.051, 34.9, 0.000), neg: 27436 (%2.337:%3.96), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 93073 --> 93081) face area 0.02 +- 0.06 (-0.21-->2.72) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
338: dt: 107.53, sse: 1470.7 (0.051, 34.6, 0.000), neg: 26824 (%1.951:%3.54), avgs: 32 scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.782, avgs=0 005/300: dt: 0.9000, rms radial error=177.523, avgs=0 010/300: dt: 0.9000, rms radial error=176.967, avgs=0 015/300: dt: 0.9000, rms radial error=176.237, avgs=0 020/300: dt: 0.9000, rms radial error=175.406, avgs=0 025/300: dt: 0.9000, rms radial error=174.516, avgs=0 030/300: dt: 0.9000, rms radial error=173.592, avgs=0 035/300: dt: 0.9000, rms radial error=172.654, avgs=0 040/300: dt: 0.9000, rms radial error=171.710, avgs=0 045/300: dt: 0.9000, rms radial error=170.765, avgs=0 050/300: dt: 0.9000, rms radial error=169.821, avgs=0 055/300: dt: 0.9000, rms radial error=168.881, avgs=0 060/300: dt: 0.9000, rms radial error=167.944, avgs=0 065/300: dt: 0.9000, rms radial error=167.011, avgs=0 070/300: dt: 0.9000, rms radial error=166.083, avgs=0 075/300: dt: 0.9000, rms radial error=165.160, avgs=0 080/300: dt: 0.9000, rms radial error=164.243, avgs=0 085/300: dt: 0.9000, rms radial error=163.332, avgs=0 090/300: dt: 0.9000, rms radial error=162.426, avgs=0 095/300: dt: 0.9000, rms radial error=161.525, avgs=0 100/300: dt: 0.9000, rms radial error=160.628, avgs=0 105/300: dt: 0.9000, rms radial error=159.737, avgs=0 110/300: dt: 0.9000, rms radial error=158.850, avgs=0 115/300: dt: 0.9000, rms radial error=157.968, avgs=0 120/300: dt: 0.9000, rms radial error=157.091, avgs=0 125/300: dt: 0.9000, rms radial error=156.218, avgs=0 130/300: dt: 0.9000, rms radial error=155.350, avgs=0 135/300: dt: 0.9000, rms radial error=154.488, avgs=0 140/300: dt: 0.9000, rms radial error=153.631, avgs=0 145/300: dt: 0.9000, rms radial error=152.778, avgs=0 150/300: dt: 0.9000, rms radial error=151.929, avgs=0 155/300: dt: 0.9000, rms radial error=151.086, avgs=0 160/300: dt: 0.9000, rms radial error=150.246, avgs=0 165/300: dt: 0.9000, rms radial error=149.411, avgs=0 170/300: dt: 0.9000, rms radial error=148.581, avgs=0 175/300: dt: 0.9000, rms radial error=147.754, avgs=0 180/300: dt: 0.9000, rms radial error=146.933, avgs=0 185/300: dt: 0.9000, rms radial error=146.115, avgs=0 190/300: dt: 0.9000, rms radial error=145.302, avgs=0 195/300: dt: 0.9000, rms radial error=144.493, avgs=0 200/300: dt: 0.9000, rms radial error=143.688, avgs=0 205/300: dt: 0.9000, rms radial error=142.888, avgs=0 210/300: dt: 0.9000, rms radial error=142.091, avgs=0 215/300: dt: 0.9000, rms radial error=141.299, avgs=0 220/300: dt: 0.9000, rms radial error=140.511, avgs=0 225/300: dt: 0.9000, rms radial error=139.727, avgs=0 230/300: dt: 0.9000, rms radial error=138.948, avgs=0 235/300: dt: 0.9000, rms radial error=138.172, avgs=0 240/300: dt: 0.9000, rms radial error=137.401, avgs=0 245/300: dt: 0.9000, rms radial error=136.634, avgs=0 250/300: dt: 0.9000, rms radial error=135.871, avgs=0 255/300: dt: 0.9000, rms radial error=135.112, avgs=0 260/300: dt: 0.9000, rms radial error=134.358, avgs=0 265/300: dt: 0.9000, rms radial error=133.607, avgs=0 270/300: dt: 0.9000, rms radial error=132.860, avgs=0 275/300: dt: 0.9000, rms radial error=132.118, avgs=0 280/300: dt: 0.9000, rms radial error=131.379, avgs=0 285/300: dt: 0.9000, rms radial error=130.645, avgs=0 290/300: dt: 0.9000, rms radial error=129.914, avgs=0 295/300: dt: 0.9000, rms radial error=129.188, avgs=0 300/300: dt: 0.9000, rms radial error=128.465, avgs=0
spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 8624.98 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.02/37 = 0.00056 epoch 2 (K=80.0), pass 1, starting sse = 1491.66 integrating with navgs=32 and tol=3.200e+00 taking m339: dt: 0.29, sse: 1470.4 (0.051, 34.7, 0.000), neg: 26880 (%1.943:%3.54), avgs: 32 340: dt: 0.29, sse: 1470.0 (0.051, 34.7, 0.000), neg: 26948 (%1.935:%3.54), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.68) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.75) 341: dt: 0.29, sse: 1469.7 (0.051, 34.7, 0.000), neg: 27043 (%1.927:%3.55), avgs: 32 342: dt: 0.29, sse: 1469.3 (0.051, 34.7, 0.000), neg: 27089 (%1.919:%3.55), avgs: 32 343: dt: 0.29, sse: 1468.9 (0.051, 34.7, 0.000), neg: 27143 (%1.911:%3.55), avgs: 32 344: dt: 0.29, sse: 1468.5 (0.051, 34.7, 0.000), neg: 27154 (%1.903:%3.55), avgs: 32 345: dt: 0.29, sse: 1467.9 (0.051, 34.7, 0.000), neg: 27168 (%1.892:%3.54), avgs: 32 346: dt: 0.29, sse: 1467.6 (0.051, 34.7, 0.000), neg: 27200 (%1.886:%3.53), avgs: 32 347: dt: 0.29, sse: 1467.3 (0.051, 34.7, 0.000), neg: 27216 (%1.879:%3.53), avgs: 32 348: dt: 0.29, sse: 1466.8 (0.051, 34.7, 0.000), neg: 27228 (%1.870:%3.52), avgs: 32 349: dt: 36.97, sse: 1459.2 (0.051, 34.6, 0.000), neg: 27004 (%1.742:%3.40), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->21.80) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.79) 350: dt: 4.85, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27064 (%1.688:%3.39), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.81) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.21-->2.79) 351: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27067 (%1.685:%3.39), avgs: 8 352: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27083 (%1.684:%3.39), avgs: 8 353: dt: 0.15, sse: 1455.9 (0.051, 34.6, 0.000), neg: 27080 (%1.681:%3.37), avgs: 8 354: dt: 0.15, sse: 1456.3 (0.051, 34.6, 0.000), neg: 27102 (%1.684:%3.38), avgs: 8 355: dt: 0.15, sse: 1456.2 (0.051, 34.6, 0.000), neg: 27124 (%1.681:%3.37), avgs: 8 356: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27155 (%1.679:%3.37), avgs: 8 357: dt: 0.15, sse: 1456.1 (0.051, 34.6, 0.000), neg: 27182 (%1.677:%3.36), avgs: 8 358: dt: 0.15, sse: 1456.0 (0.051, 34.6, 0.000), neg: 27190 (%1.674:%3.36), avgs: 8 359: dt: 0.15, sse: 1455.8 (0.051, 34.6, 0.000), neg: 27194 (%1.669:%3.35), avgs: 8 360: dt: 0.15, sse: 1455.6 (0.051, 34.6, 0.000), neg: 27210 (%1.665:%3.35), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->21.92) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.80) 361: dt: 9.20, sse: 1452.7 (0.051, 34.6, 0.000), neg: 27182 (%1.611:%3.30), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.00) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.80) 362: dt: 0.77, sse: 1451.0 (0.051, 34.6, 0.000), neg: 27300 (%1.582:%3.32), avgs: 2 363: dt: 0.09, sse: 1450.6 (0.051, 34.6, 0.000), neg: 27301 (%1.575:%3.31), avgs: 2 364: dt: 0.09, sse: 1450.3 (0.051, 34.6, 0.000), neg: 27336 (%1.568:%3.31), avgs: 2 365: dt: 0.09, sse: 1449.7 (0.051, 34.6, 0.000), neg: 27352 (%1.556:%3.31), avgs: 2 366: dt: 0.09, sse: 1449.0 (0.051, 34.6, 0.000), neg: 27377 (%1.544:%3.32), avgs: 2 367: dt: 0.09, sse: 1448.6 (0.051, 34.6, 0.000), neg: 27398 (%1.536:%3.31), avgs: 2 368: dt: 0.09, sse: 1448.0 (0.051, 34.6, 0.000), neg: 27412 (%1.526:%3.31), avgs: 2 369: dt: 0.09, sse: 1447.4 (0.051, 34.6, 0.000), neg: 27438 (%1.514:%3.30), avgs: 2 370: dt: 0.09, sse: 1446.5 (0.051, 34.6, 0.000), neg: 27458 (%1.499:%3.30), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.08) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.14-->2.80) 371: dt: 0.09, sse: 1445.8 (0.051, 34.6, 0.000), neg: 27460 (%1.486:%3.29), avgs: 2 372: dt: 0.09, sse: 1445.1 (0.051, 34.6, 0.000), neg: 27497 (%1.474:%3.28), avgs: 2 373: dt: 1.48, sse: 1443.8 (0.051, 34.7, 0.000), neg: 27589 (%1.452:%3.29), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.12-->2.81) 374: dt: 0.27, sse: 1443.2 (0.051, 34.7, 0.000), neg: 27714 (%1.439:%3.27), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.29-->2.81) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
375: dt: 36.63, sse: 250.8 (0.051, 34.6, 0.000), neg: 27421 (%1.349:%3.19), avgs: 32 376: dt: 0.29, sse: 250.5 (0.051, 34.6, 0.000), neg: 27438 (%1.343:%3.19), avgs: 32 377: dt: 0.29, sse: 250.2 (0.051, 34.6, 0.000), neg: 27456 (%1.339:%3.18), avgs: 32 378: dt: 0.29, sse: 249.9 (0.051, 34.6, 0.000), neg: 27450 (%1.333:%3.17), avgs: 32 379: dt: 0.29, sse: 249.6 (0.051, 34.6, 0.000), neg: 27460 (%1.330:%3.16), avgs: 32 380: dt: 0.29, sse: 249.5 (0.051, 34.6, 0.000), neg: 27454 (%1.327:%3.15), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.32-->2.82) 381: dt: 0.29, sse: 249.4 (0.051, 34.6, 0.000), neg: 27446 (%1.325:%3.15), avgs: 32 382: dt: 0.29, sse: 249.2 (0.051, 34.6, 0.000), neg: 27444 (%1.322:%3.14), avgs: 32 383: dt: 0.29, sse: 249.0 (0.051, 34.6, 0.000), neg: 27438 (%1.319:%3.13), avgs: 32 384: dt: 0.29, sse: 248.9 (0.051, 34.6, 0.000), neg: 27421 (%1.317:%3.12), avgs: 32 385: dt: 0.29, sse: 248.7 (0.051, 34.6, 0.000), neg: 27418 (%1.313:%3.12), avgs: 32 386: dt: 155.64, sse: 241.3 (0.051, 34.3, 0.000), neg: 26865 (%1.190:%2.88), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.14) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.26-->2.81) 387: dt: 2.19, sse: 237.7 (0.051, 34.3, 0.000), neg: 26842 (%1.139:%2.86), avgs: 8 388: dt: 0.15, sse: 237.6 (0.051, 34.3, 0.000), neg: 26834 (%1.137:%2.87), avgs: 8 389: dt: 0.15, sse: 237.5 (0.051, 34.3, 0.000), neg: 26828 (%1.136:%2.87), avgs: 8 390: dt: 0.15, sse: 237.2 (0.051, 34.3, 0.000), neg: 26807 (%1.131:%2.86), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.18) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.27-->2.81) 391: dt: 0.15, sse: 236.9 (0.051, 34.3, 0.000), neg: 26807 (%1.126:%2.86), avgs: 8 392: dt: 0.15, sse: 236.5 (0.051, 34.3, 0.000), neg: 26810 (%1.121:%2.86), avgs: 8 393: dt: 0.15, sse: 236.2 (0.051, 34.3, 0.000), neg: 26798 (%1.116:%2.86), avgs: 8 394: dt: 0.15, sse: 235.8 (0.051, 34.3, 0.000), neg: 26789 (%1.110:%2.86), avgs: 8 395: dt: 0.15, sse: 235.5 (0.051, 34.3, 0.000), neg: 26775 (%1.105:%2.86), avgs: 8 396: dt: 0.15, sse: 235.2 (0.051, 34.3, 0.000), neg: 26753 (%1.100:%2.85), avgs: 8 397: dt: 0.15, sse: 234.8 (0.051, 34.3, 0.000), neg: 26743 (%1.094:%2.84), avgs: 8 398: dt: 15.35, sse: 232.1 (0.051, 34.2, 0.000), neg: 26547 (%1.053:%2.76), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.25-->2.82) 399: dt: 1.29, sse: 228.5 (0.051, 34.2, 0.000), neg: 26596 (%1.000:%2.76), avgs: 2 400: dt: 0.54, sse: 227.3 (0.051, 34.2, 0.000), neg: 26618 (%0.983:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.30) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.22-->2.82) 401: dt: 0.09, sse: 227.3 (0.051, 34.2, 0.000), neg: 26629 (%0.983:%2.75), avgs: 2 402: dt: 0.09, sse: 227.0 (0.051, 34.2, 0.000), neg: 26613 (%0.978:%2.75), avgs: 2 403: dt: 0.09, sse: 226.7 (0.051, 34.2, 0.000), neg: 26617 (%0.973:%2.76), avgs: 2 404: dt: 0.09, sse: 226.4 (0.051, 34.2, 0.000), neg: 26605 (%0.968:%2.76), avgs: 2 405: dt: 0.09, sse: 226.0 (0.051, 34.2, 0.000), neg: 26603 (%0.962:%2.76), avgs: 2 406: dt: 0.09, sse: 225.8 (0.051, 34.2, 0.000), neg: 26617 (%0.958:%2.77), avgs: 2 407: dt: 0.09, sse: 225.4 (0.051, 34.2, 0.000), neg: 26612 (%0.953:%2.77), avgs: 2 408: dt: 0.09, sse: 225.1 (0.051, 34.2, 0.000), neg: 26604 (%0.948:%2.77), avgs: 2 409: dt: 0.09, sse: 224.8 (0.051, 34.1, 0.000), neg: 26602 (%0.943:%2.76), avgs: 2 410: dt: 0.09, sse: 224.4 (0.051, 34.1, 0.000), neg: 26606 (%0.937:%2.75), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.35) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 411: dt: 1.71, sse: 223.5 (0.051, 34.1, 0.000), neg: 26591 (%0.925:%2.71), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) 412: dt: 0.03, sse: 223.1 (0.051, 34.1, 0.000), neg: 26666 (%0.918:%2.72), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.37) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.20-->2.83) tol=1.8e+01, sigma=0.0, host=local, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization
413: dt: 48.76, sse: 83.1 (0.051, 34.1, 0.000), neg: 26317 (%0.904:%2.68), avgs: 32 414: dt: 0.29, sse: 82.8 (0.051, 34.0, 0.000), neg: 26321 (%0.900:%2.68), avgs: 32 415: dt: 0.29, sse: 82.5 (0.051, 34.0, 0.000), neg: 26315 (%0.895:%2.68), avgs: 32 416: dt: 0.29, sse: 82.1 (0.051, 34.0, 0.000), neg: 26291 (%0.889:%2.67), avgs: 32 417: dt: 0.29, sse: 81.8 (0.051, 34.0, 0.000), neg: 26274 (%0.885:%2.67), avgs: 32 418: dt: 0.29, sse: 81.4 (0.051, 34.0, 0.000), neg: 26258 (%0.880:%2.66), avgs: 32 419: dt: 0.29, sse: 81.0 (0.051, 34.0, 0.000), neg: 26222 (%0.875:%2.65), avgs: 32 420: dt: 0.29, sse: 80.8 (0.051, 34.0, 0.000), neg: 26202 (%0.872:%2.64), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.29) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.23-->2.84) 421: dt: 0.29, sse: 80.6 (0.051, 34.0, 0.000), neg: 26208 (%0.868:%2.64), avgs: 32 422: dt: 0.29, sse: 80.4 (0.051, 34.0, 0.000), neg: 26186 (%0.866:%2.64), avgs: 32 423: dt: 0.29, sse: 80.2 (0.051, 34.0, 0.000), neg: 26174 (%0.863:%2.64), avgs: 32 424: dt: 42.80, sse: 78.6 (0.051, 34.0, 0.000), neg: 26068 (%0.840:%2.60), avgs: 32 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.84) 425: dt: 1.85, sse: 78.2 (0.051, 34.0, 0.000), neg: 26076 (%0.834:%2.57), avgs: 8 426: dt: 0.15, sse: 78.1 (0.051, 34.0, 0.000), neg: 26074 (%0.832:%2.57), avgs: 8 427: dt: 0.15, sse: 77.7 (0.051, 34.0, 0.000), neg: 26071 (%0.828:%2.57), avgs: 8 428: dt: 0.15, sse: 77.6 (0.051, 34.0, 0.000), neg: 26057 (%0.826:%2.57), avgs: 8 429: dt: 0.15, sse: 77.4 (0.051, 33.9, 0.000), neg: 26034 (%0.823:%2.57), avgs: 8 430: dt: 0.15, sse: 76.9 (0.051, 33.9, 0.000), neg: 26021 (%0.817:%2.56), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.12) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 431: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26008 (%0.814:%2.57), avgs: 8 432: dt: 0.15, sse: 76.8 (0.051, 33.9, 0.000), neg: 26015 (%0.814:%2.58), avgs: 8 433: dt: 0.15, sse: 76.5 (0.051, 33.9, 0.000), neg: 25996 (%0.811:%2.57), avgs: 8 434: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25991 (%0.808:%2.57), avgs: 8 435: dt: 0.15, sse: 76.3 (0.051, 33.9, 0.000), neg: 25997 (%0.808:%2.58), avgs: 8 436: dt: 1.20, sse: 76.2 (0.051, 33.9, 0.000), neg: 25992 (%0.805:%2.57), avgs: 8 vertex spacing 0.98 +- 0.89 (0.00-->22.13) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.11-->2.85) 437: dt: 1.30, sse: 75.7 (0.051, 33.9, 0.000), neg: 26032 (%0.797:%2.57), avgs: 2 438: dt: 0.09, sse: 75.5 (0.051, 33.9, 0.000), neg: 26022 (%0.795:%2.57), avgs: 2 439: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26010 (%0.789:%2.56), avgs: 2 440: dt: 0.09, sse: 75.1 (0.051, 33.9, 0.000), neg: 26003 (%0.788:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.16) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.10-->2.85) 441: dt: 0.09, sse: 74.9 (0.051, 33.9, 0.000), neg: 26008 (%0.786:%2.57), avgs: 2 442: dt: 0.09, sse: 74.7 (0.051, 33.9, 0.000), neg: 26002 (%0.783:%2.57), avgs: 2 443: dt: 0.09, sse: 74.5 (0.051, 33.9, 0.000), neg: 26006 (%0.780:%2.58), avgs: 2 444: dt: 0.09, sse: 74.2 (0.051, 33.9, 0.000), neg: 26014 (%0.775:%2.58), avgs: 2 445: dt: 0.09, sse: 73.9 (0.051, 33.9, 0.000), neg: 26031 (%0.771:%2.58), avgs: 2 446: dt: 0.09, sse: 73.8 (0.051, 33.9, 0.000), neg: 26044 (%0.769:%2.59), avgs: 2 447: dt: 0.09, sse: 73.7 (0.051, 33.9, 0.000), neg: 26058 (%0.767:%2.61), avgs: 2 448: dt: 1.25, sse: 73.3 (0.051, 33.8, 0.000), neg: 25993 (%0.761:%2.57), avgs: 2 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.19-->2.85) 449: dt: 0.03, sse: 73.2 (0.051, 33.8, 0.000), neg: 26076 (%0.760:%2.60), avgs: 0 vertex spacing 0.98 +- 0.89 (0.00-->22.22) (max @ vno 89761 --> 90895) face area 0.02 +- 0.06 (-0.18-->2.85) 449: dt: 0.00, sse: 8423.5 (0.050, 33.8, 0.000), neg: 26076 (%0.754:%2.60), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours omentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.03/37 = 0.00088 epoch 3 (K=320.0), pass 1, starting sse = 256.64 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/38 = 0.00344 epoch 4 (K=1280.0), pass 1, starting sse = 83.95 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.13/37 = 0.00346 final distance error %100000.00 optimization complete. unfolding took 0.12 hours #-------------------------------------------- #@# Fix Topology lh Wed Mar 3 22:34:46 CET 2010
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/home/kutato/freesurfer/subjects/C1/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga C1 lh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters
Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $ before topology correction, eno=-408 (nv=152952, nf=306720, ne=460080, g=205) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 56276 ambiguous faces found in tessellation segmenting defects... 92 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 4 -merging segment 0 into 5 -merging segment 29 into 27 -merging segment 32 into 30 -merging segment 71 into 49 -merging segment 4 into 52 -merging segment 74 into 72 85 defects to be corrected 0 vertices coincident reading input surface /home/kutato/freesurfer/subjects/C1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1015 (-4.5508) -vertex loglikelihood: -6.5092 (-3.2546) -normal dot loglikelihood: -3.5881 (-3.5881) -quad curv loglikelihood: -5.9652 (-2.9826) Total Loglikelihood : -25.1641
CORRECTING DEFECT 0 (vertices=48, convex hull=73) After retessellation of defect 0, euler #=-66 (121738,358994,237190) : difference with theory (-82) = -16
CORRECTING DEFECT 1 (vertices=172, convex hull=59) After retessellation of defect 1, euler #=-65 (121763,359092,237264) : difference with theory (-81) = -16
CORRECTING DEFECT 2 (vertices=14, convex hull=14) After retessellation of defect 2, euler #=-64 (121763,359095,237268) : difference with theory (-80) = -16
CORRECTING DEFECT 3 (vertices=4413, convex hull=721) After retessellation of defect 3, euler #=-67 (122638,362153,239448) : difference with theory (-79) = -12
CORRECTING DEFECT 4 (vertices=16, convex hull=21) After retessellation of defect 4, euler #=-66 (122639,362162,239457) : difference with theory (-78) = -12
CORRECTING DEFECT 5 (vertices=318, convex hull=123) After retessellation of defect 5, euler #=-65 (122682,362353,239606) : difference with theory (-77) = -12
CORRECTING DEFECT 6 (vertices=39, convex hull=81) After retessellation of defect 6, euler #=-64 (122698,362433,239671) : difference with theory (-76) = -12
CORRECTING DEFECT 7 (vertices=43, convex hull=30) After retessellation of defect 7, euler #=-63 (122702,362458,239693) : difference with theory (-75) = -12
CORRECTING DEFECT 8 (vertices=87, convex hull=103) After retessellation of defect 8, euler #=-62 (122736,362601,239803) : difference with theory (-74) = -12
CORRECTING DEFECT 9 (vertices=22, convex hull=52) After retessellation of defect 9, euler #=-61 (122744,362644,239839) : difference with theory (-73) = -12
CORRECTING DEFECT 10 (vertices=103, convex hull=78) After retessellation of defect 10, euler #=-60 (122768,362752,239924) : difference with theory (-72) = -12
CORRECTING DEFECT 11 (vertices=427, convex hull=253) After retessellation of defect 11, euler #=-59 (122927,363356,240370) : difference with theory (-71) = -12
CORRECTING DEFECT 12 (vertices=1508, convex hull=562) After retessellation of defect 12, euler #=-59 (123340,364897,241498) : difference with theory (-70) = -11
CORRECTING DEFECT 13 (vertices=57, convex hull=109) After retessellation of defect 13, euler #=-58 (123374,365043,241611) : difference with theory (-69) = -11
CORRECTING DEFECT 14 (vertices=49, convex hull=79) After retessellation of defect 14, euler #=-57 (123402,365159,241700) : difference with theory (-68) = -11
CORRECTING DEFECT 15 (vertices=69, convex hull=96) After retessellation of defect 15, euler #=-56 (123431,365288,241801) : difference with theory (-67) = -11
CORRECTING DEFECT 16 (vertices=29, convex hull=55) After retessellation of defect 16, euler #=-55 (123440,365339,241844) : difference with theory (-66) = -11
CORRECTING DEFECT 17 (vertices=14, convex hull=28) After retessellation of defect 17, euler #=-54 (123443,365354,241857) : difference with theory (-65) = -11
CORRECTING DEFECT 18 (vertices=41, convex hull=48) After retessellation of defect 18, euler #=-53 (123452,365398,241893) : difference with theory (-64) = -11
CORRECTING DEFECT 19 (vertices=459, convex hull=241) After retessellation of defect 19, euler #=-52 (123590,365935,242293) : difference with theory (-63) = -11
CORRECTING DEFECT 20 (vertices=55, convex hull=110) After retessellation of defect 20, euler #=-51 (123623,366080,242406) : difference with theory (-62) = -11
CORRECTING DEFECT 21 (vertices=478, convex hull=255) After retessellation of defect 21, euler #=-50 (123653,366319,242616) : difference with theory (-61) = -11
CORRECTING DEFECT 22 (vertices=27, convex hull=34) After retessellation of defect 22, euler #=-49 (123662,366357,242646) : difference with theory (-60) = -11
CORRECTING DEFECT 23 (vertices=53, convex hull=92) After retessellation of defect 23, euler #=-48 (123692,366487,242747) : difference with theory (-59) = -11
CORRECTING DEFECT 24 (vertices=32, convex hull=45) After retessellation of defect 24, euler #=-46 (123692,366504,242766) : difference with theory (-58) = -12
CORRECTING DEFECT 25 (vertices=181, convex hull=167) After retessellation of defect 25, euler #=-45 (123711,366644,242888) : difference with theory (-57) = -12
CORRECTING DEFECT 26 (vertices=1122, convex hull=340) After retessellation of defect 26, euler #=-45 (124058,367886,243783) : difference with theory (-56) = -11
CORRECTING DEFECT 27 (vertices=213, convex hull=67) After retessellation of defect 27, euler #=-44 (124080,367986,243862) : difference with theory (-55) = -11
CORRECTING DEFECT 28 (vertices=35, convex hull=22) After retessellation of defect 28, euler #=-43 (124085,368007,243879) : difference with theory (-54) = -11
CORRECTING DEFECT 29 (vertices=20, convex hull=63) After retessellation of defect 29, euler #=-42 (124095,368059,243922) : difference with theory (-53) = -11
CORRECTING DEFECT 30 (vertices=13, convex hull=26) After retessellation of defect 30, euler #=-41 (124096,368072,243935) : difference with theory (-52) = -11
CORRECTING DEFECT 31 (vertices=29, convex hull=74) After retessellation of defect 31, euler #=-40 (124105,368127,243982) : difference with theory (-51) = -11
CORRECTING DEFECT 32 (vertices=42, convex hull=33) After retessellation of defect 32, euler #=-39 (124109,368148,244000) : difference with theory (-50) = -11
CORRECTING DEFECT 33 (vertices=88, convex hull=93) After retessellation of defect 33, euler #=-38 (124124,368233,244071) : difference with theory (-49) = -11
CORRECTING DEFECT 34 (vertices=53, convex hull=67) After retessellation of defect 34, euler #=-37 (124137,368300,244126) : difference with theory (-48) = -11
CORRECTING DEFECT 35 (vertices=396, convex hull=152) After retessellation of defect 35, euler #=-36 (124283,368807,244488) : difference with theory (-47) = -11
CORRECTING DEFECT 36 (vertices=49, convex hull=71) After retessellation of defect 36, euler #=-35 (124310,368918,244573) : difference with theory (-46) = -11
CORRECTING DEFECT 37 (vertices=6, convex hull=20) After retessellation of defect 37, euler #=-34 (124311,368926,244581) : difference with theory (-45) = -11
CORRECTING DEFECT 38 (vertices=42, convex hull=81) After retessellation of defect 38, euler #=-33 (124337,369038,244668) : difference with theory (-44) = -11
CORRECTING DEFECT 39 (vertices=96, convex hull=66) After retessellation of defect 39, euler #=-32 (124378,369192,244782) : difference with theory (-43) = -11
CORRECTING DEFECT 40 (vertices=27, convex hull=34) After retessellation of defect 40, euler #=-31 (124382,369214,244801) : difference with theory (-42) = -11
CORRECTING DEFECT 41 (vertices=295, convex hull=174) After retessellation of defect 41, euler #=-30 (124455,369519,245034) : difference with theory (-41) = -11
CORRECTING DEFECT 42 (vertices=192, convex hull=126) After retessellation of defect 42, euler #=-29 (124483,369662,245150) : difference with theory (-40) = -11
CORRECTING DEFECT 43 (vertices=100, convex hull=110) After retessellation of defect 43, euler #=-28 (124549,369912,245335) : difference with theory (-39) = -11
CORRECTING DEFECT 44 (vertices=564, convex hull=398) After retessellation of defect 44, euler #=-27 (124766,370766,245973) : difference with theory (-38) = -11
CORRECTING DEFECT 45 (vertices=148, convex hull=121) After retessellation of defect 45, euler #=-26 (124843,371049,246180) : difference with theory (-37) = -11
CORRECTING DEFECT 46 (vertices=51, convex hull=75) After retessellation of defect 46, euler #=-25 (124855,371114,246234) : difference with theory (-36) = -11
CORRECTING DEFECT 47 (vertices=16122, convex hull=4397) normal vector of length zero at vertex 139578 with 0 faces vertex 139578 has 0 face Numerical result out of range Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 4 05:39:45 CET 2010
2010/3/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Gabor,
recon2-cp currently starts *after* the aseg, so you'll need to rerun it from an ealier point than that. Try using -autorecon2 instead.
cheers Bruce
On Wed, 3 Mar 2010, Perlaki Gabor wrote:
Hi all!
We overlayed the aseg.mgz on the norm.mgz and put some controll points where the cerebellum segmentation was not accurate and we saved the controll points. We reran recon-all like this: 'recon-all -autorecon2-cp -autorecon3 -subjid our_subj' After that we checked the volume of cerebellum, and it is the same as it was before the whole procedure, and aseg.mgz is the same as well. How can we check that how accurate the segmentation of cerebellum after the reran of recon-all, and where are the new results?
Thank you very much,
Gabor Perlaki
On Fri, 26 Feb 2010 08:49:48 -0500 (EST), Bruce Fischl wrote
Hi Gergely,
overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stuff through FSL or SPM VMB though.
cheers, Bruce
On Fri, 26 Feb 2010, Gergely Orsi wrote:
Hi all! > > We have processed 100 subjects with autorecon. > I'd like to know how to check the cerebellum segmentation on the > subjects. It would be crucial, because the images are a bit dimmer at > the > lower areas (it's far from the isocenter) and despite the intensity > normalisation it still has lower intensity compared to the dorsal part > of > the cerebellum. After the skull-strip the cerebellum is still intact > (the > whole cerebellum exists on the images), but I'd like to know wether > freesurfer recognised the lower intensity parts or not. > > Unfortunatly BET in FSL simply cut off these areas, thus our VBM results > (showing significan changes at the ventral cerebellum) are compromised. > > We have measured significant group differences in total cerebellar > volume > using freesurfer, but we should check the segmentation first, and > believe > the results later. > > Could anyone help us in this? > > And if the segmentation failed, is there any manual method to correct it > (by > hand), because the whole cerebellum is on the images (despite of the > different intensity). > > And one last question, is it possible to carry out VBM in freesurfer > (after > checking/correcting the cerebellum if needed, although the intensity > difference will still be a big problem in VBM ). > > > Thank you very much. > > > > Gergely Orsi > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Pécsi Tudományegyetem Természettudományi Kar (http://www.ttk.pte.hu/)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gergely Orsi -
Perlaki Gabor