Wed Nov 10 10:42:35 CET 2010 /home/falk/freesurfer/subjects/test_shan /usr/share/freesurfer/bin/recon-all -cm -autorecon1 -i mprage.nii -s test_shan -nuintensitycor-3T subjid test_shan setenv SUBJECTS_DIR /home/falk/freesurfer/subjects FREESURFER_HOME /usr/share/freesurfer Actual FREESURFER_HOME /usr/share/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux bmmr-56723 2.6.26-2-amd64 #1 SMP Thu Nov 5 02:23:12 UTC 2009 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 270336 total used free shared buffers cached Mem: 33023316 25903456 7119860 0 276404 15716372 -/+ buffers/cache: 9910680 23112636 Swap: 31720292 31169676 550616 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 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 2010-02-20 at 17:32:37 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:35-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:36-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:37-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2010/11/10-09:42:38-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: falk Machine: bmmr-56723 Platform: Linux PlatformVersion: 2.6.26-2-amd64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/share/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/share/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/falk/freesurfer/subjects/test_shan mri_convert /home/falk/data/test/mprage.nii /home/falk/freesurfer/subjects/test_shan/mri/orig/001.mgz mri_convert /home/falk/data/test/mprage.nii /home/falk/freesurfer/subjects/test_shan/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/falk/data/test/mprage.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0540789, 0, 0.998537) k_ras = (0.998537, 0, 0.0540789) writing to /home/falk/freesurfer/subjects/test_shan/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Nov 10 10:42:45 CET 2010 Found 1 runs /home/falk/freesurfer/subjects/test_shan/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/falk/freesurfer/subjects/test_shan/mri/orig/001.mgz /home/falk/freesurfer/subjects/test_shan/mri/rawavg.mgz /home/falk/freesurfer/subjects/test_shan mri_convert /home/falk/freesurfer/subjects/test_shan/mri/rawavg.mgz /home/falk/freesurfer/subjects/test_shan/mri/orig.mgz --conform_min mri_convert /home/falk/freesurfer/subjects/test_shan/mri/rawavg.mgz /home/falk/freesurfer/subjects/test_shan/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/falk/freesurfer/subjects/test_shan/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0540789, 0, 0.998537) k_ras = (0.998537, 0, 0.0540789) Original Data has (0.7, 0.7, 0.7) mm size and (320, 320, 224) voxels. Data is conformed to 0.7 mm size and 321 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/falk/freesurfer/subjects/test_shan/mri/orig.mgz... mri_add_xform_to_header -c /home/falk/freesurfer/subjects/test_shan/mri/transforms/talairach.xfm /home/falk/freesurfer/subjects/test_shan/mri/orig.mgz /home/falk/freesurfer/subjects/test_shan/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Wed Nov 10 10:43:15 CET 2010 mri_nu_correct.mni --i orig.mgz --o nu.mgz --proto-iters 1000 --distance 50 --n 1 /home/falk/freesurfer/subjects/test_shan/mri /usr/share/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux bmmr-56723 2.6.26-2-amd64 #1 SMP Thu Nov 5 02:23:12 UTC 2009 x86_64 GNU/Linux Wed Nov 10 10:43:15 CET 2010 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.32343 /home/falk/freesurfer/subjects/test_shan/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32343/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32343/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 2.12874e-08) j_ras = (3.72529e-08, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.32343/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Wed Nov 10 10:43:50 CET 2010 nu_correct -clobber ./tmp.mri_nu_correct.mni.32343/nu0.mnc ./tmp.mri_nu_correct.mni.32343/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.32343/0/ -iterations 1000 -distance 50 [falk@bmmr-56723:/home/falk/freesurfer/subjects/test_shan/mri/] [2010-11-10 10:43:50] running: /usr/share/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.32343/0/ ./tmp.mri_nu_correct.mni.32343/nu0.mnc ./tmp.mri_nu_correct.mni.32343/nu1.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 21 CV of field change: 0.000984105 [falk@bmmr-56723:/home/falk/freesurfer/subjects/test_shan/mri/] [2010-11-10 10:44:27] running: /usr/share/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.32343/nu0.mnc ./tmp.mri_nu_correct.mni.32343/0//template.mnc Transforming slices:............................................................................................................Done Transforming slices:.................................................................................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.32343/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32343/ones.mgz $Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $ cwd /home/falk/freesurfer/subjects/test_shan/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.32343/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32343/ones.mgz sysname Linux hostname bmmr-56723 machine x86_64 user falk input ./tmp.mri_nu_correct.mni.32343/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.32343/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 33076161 values in range Counting number of voxels Found 33076161 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32343/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32343/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32343/input.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32343/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32343/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32343/input.mean.dat sysname Linux hostname bmmr-56723 machine x86_64 user falk Loading ./tmp.mri_nu_correct.mni.32343/ones.mgz Loading orig.mgz Voxel Volume is 0.343 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 33076161 1.13451e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.32343/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32343/ones.mgz --i ./tmp.mri_nu_correct.mni.32343/nu1.mnc --sum ./tmp.mri_nu_correct.mni.32343/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32343/output.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32343/ones.mgz --i ./tmp.mri_nu_correct.mni.32343/nu1.mnc --sum ./tmp.mri_nu_correct.mni.32343/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32343/output.mean.dat sysname Linux hostname bmmr-56723 machine x86_64 user falk Loading ./tmp.mri_nu_correct.mni.32343/ones.mgz Loading ./tmp.mri_nu_correct.mni.32343/nu1.mnc Voxel Volume is 0.343 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 33076161 1.13451e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.32343/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.32343/nu1.mnc ./tmp.mri_nu_correct.mni.32343/nu1.mnc mul 1.01460140911529667100 Saving result to './tmp.mri_nu_correct.mni.32343/nu1.mnc' (type=3)Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.32343/nu1.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.32343/nu1.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.32343/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 2.12874e-08) j_ras = (3.72529e-08, 0, -1) k_ras = (0, 1, 0) Original Data has (0.7, 0.7, 0.7) mm size and (321, 321, 321) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to nu.mgz... Wed Nov 10 10:47:32 CET 2010 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Wed Nov 10 10:47:32 CET 2010 /home/falk/freesurfer/subjects/test_shan/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Nov 10 10:48:28 CET 2010 /home/falk/freesurfer/subjects/test_shan/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5580, pval=0.2115 >= threshold=0.0050) awk -f /usr/share/freesurfer/bin/extract_talairach_avi_QA.awk /home/falk/freesurfer/subjects/test_shan/mri/transforms/talairach_avi.log TalAviQA: 0.96406 z-score: -3 #-------------------------------------------- #@# Intensity Normalization Wed Nov 10 10:48:28 CET 2010 /home/falk/freesurfer/subjects/test_shan/mri mri_normalize -g 1 -noconform nu.mgz T1.mgz using max gradient = 1.000 not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... building Voronoi diagram...