Fri Oct 20 10:53:25 EDT 2006 /yjet/grosspeople/jon_adaptation/freesurfer/303 /home/peelle/freesurfer/bin/recon-all -autorecon2 -subjid 303 subjid 303 setenv SUBJECTS_DIR /yjet/grosspeople/jon_adaptation/freesurfer FREESURFER_HOME /home/peelle/freesurfer/ Actual FREESURFER_HOME /home/peelle/freesurfer Linux echo.uphs.upenn.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 16375 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:25-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:26-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:27-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:28-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/20-14:53:28-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: peelle Machine: echo.uphs.upenn.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #------------------------------------- #@# EM Registration Fri Oct 20 10:53:28 EDT 2006 /yjet/grosspeople/jon_adaptation/freesurfer/303/mri mri_em_register -mask brainmask.mgz nu.mgz /home/peelle/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/peelle/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (0.6, -11.9, -5.1): log p = -34245.2 Result so far: scale 1.000: max_log_p=-17481.2, old_max_log_p =-34245.2 (thresh=-34210.9) 1.184 0.023 -0.165 -7.466; 0.000 1.184 0.166 -54.218; 0.147 -0.145 1.034 -8.437; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-16638.7, old_max_log_p =-17481.2 (thresh=-17463.7) 1.110 0.022 -0.154 0.918; 0.000 1.258 0.177 -65.013; 0.147 -0.145 1.034 -8.437; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-16638.7, old_max_log_p =-16638.7 (thresh=-16622.1) 1.110 0.022 -0.154 0.918; 0.000 1.258 0.177 -65.013; 0.147 -0.145 1.034 -8.437; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10970 0.02171 -0.15444 0.91756; 0.00000 1.25766 0.17675 -65.01289; 0.14678 -0.14536 1.03426 -8.43713; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.10970 0.02171 -0.15444 0.91756; 0.00000 1.25766 0.17675 -65.01289; 0.14678 -0.14536 1.03426 -8.43713; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... fp = 15819.927734, fret = 15819.927734, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10970 0.02171 -0.15444 0.91756; 0.00000 1.25766 0.17675 -65.01289; 0.14678 -0.14536 1.03426 -8.43713; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.10970 0.02171 -0.15444 0.91756; 0.00000 1.25766 0.17675 -65.01289; 0.14678 -0.14536 1.03426 -8.43713; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... pass 5 through quasi-newton minimization... pass 6 through quasi-newton minimization... freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ Note: program considers input volume #1 as the most T1-like using real data threshold=29.0 using (103, 112, 121) as brain centroid... mean wm in atlas = 109, using box (87,98,100) --> (118, 126,141) to find MRI wm before smoothing, mri peak at 129 after smoothing, mri peak at 128, scaling input intensities by 0.851 scaling channel 0 by 0.850552 initial log_p = -51991.0 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 003: -log(p) = 16638.7 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.18, -65.01) ( 0.15, -0.15, 1.03, -8.44) dfp_em_step_func: 004: -log(p) = 15927.1 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( -0.00, 1.25, 0.17, -65.01) ( 0.14, -0.15, 1.03, -8.44) dfp_em_step_func: 005: -log(p) = 15819.9 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( -0.00, 1.25, 0.17, -65.01) ( 0.14, -0.15, 1.03, -8.44) outof QuasiNewtonEMA: 007: -log(p) = 15819.9 tol 0.000010 Resulting transform: 1.110 0.022 -0.154 0.918; 0.000 1.258 0.177 -65.013; 0.147 -0.145 1.034 -8.437; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -16638.7 (old=-51991.0) transform before final EM align: 1.110 0.022 -0.154 0.918; 0.000 1.258 0.177 -65.013; 0.147 -0.145 1.034 -8.437; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 006: -log(p) = 1806251.0 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.18, -65.01) ( 0.15, -0.15, 1.03, -8.44) dfp_em_step_func: 007: -log(p) = 1774161.2 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.18, -65.01) ( 0.15, -0.15, 1.03, -8.44) dfp_em_step_func: 008: -log(p) = 1753445.5 after pass:transform: ( 1.12, 0.03, -0.14, 0.92) ( 0.00, 1.26, 0.18, -65.01) ( 0.14, -0.15, 1.03, -8.44) dfp_em_step_func: 009: -log(p) = 1710744.5 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.17, -65.01) ( 0.14, -0.15, 1.03, -8.44) dfp_em_step_func: 010: -log(p) = 1705151.0 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.17, -65.01) ( 0.14, -0.15, 1.03, -8.44) dfp_em_step_func: 011: -log(p) = 1703543.0 after pass:transform: ( 1.11, 0.02, -0.15, 0.92) ( 0.00, 1.26, 0.17, -65.01) ( 0.14, -0.15, 1.03, -8.44) outof QuasiNewtonEMA: 013: -log(p) = 1698678.5 tol 0.000000 final transform: 1.115 0.024 -0.147 0.918; 0.002 1.257 0.172 -65.013; 0.141 -0.149 1.033 -8.437; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 23 minutes and 26 seconds. #-------------------------------------- #@# CA Normalize Fri Oct 20 11:16:54 EDT 2006 /yjet/grosspeople/jon_adaptation/freesurfer/303/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /home/peelle/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/peelle/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.115 0.024 -0.147 0.918; 0.002 1.257 0.172 -65.013; 0.141 -0.149 1.033 -8.437; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=29.0 using (103, 112, 121) as brain centroid... mean wm in atlas = 109, using box (87,98,100) --> (118, 126,141) to find MRI wm before smoothing, mri peak at 129 after smoothing, mri peak at 128, scaling input intensities by 0.851 scaling channel 0 by 0.850552 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (114, 80, 37) --> (181, 168, 193) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 114.0 94 of 348 (27.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (66, 80, 40) --> (131, 168, 196) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 117.0 136 of 484 (28.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (120, 150, 60) --> (163, 183, 112) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 115.0 16 of 57 (28.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (79, 151, 63) --> (121, 182, 116) Right_Cerebellum_White_Matter: limiting intensities to 110.0 --> 126.0 15 of 66 (22.7%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (108, 138, 95) --> (138, 195, 125) Brain_Stem: limiting intensities to 97.0 --> 115.0 34 of 107 (31.8%) samples deleted using 1062 total control points for intensity normalization... bias field = 1.005 +- 0.115 0 of 767 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 3 minutes and 57 seconds. #-------------------------------------- #@# CA Reg Fri Oct 20 11:20:52 EDT 2006 /yjet/grosspeople/jon_adaptation/freesurfer/303/mri mri_ca_register -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /home/peelle/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.m3z renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/peelle/freesurfer/average/RB_all_2006-02-15.gca'... Killed ERROR: mri_ca_register with non-zero status Linux echo.uphs.upenn.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Oct 20 11:23:58 EDT 2006