Is usually just a symlink to $FREESURFER_HOME/subjects/fsaverage Does that exist? If its empty you'll have to download again Cheers Bruce
On Jun 25, 2013, at 9:31 PM, Salil Soman salsoman@stanford.edu wrote:
Dear Bruce,
I apologize, I misread your last message. My fsaverage folder is now empty. We had some issues with storage space for our output files and I am rerunning a number of patients for a different study from the ones I had done previously (but acquired with the same protocol). I guess these files got lost. Is there a way I can reset my freesurfer install to function as though I am running cases for the first time / get things working again?
Best wishes,
Sal
On Tue, Jun 25, 2013 at 6:25 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: those are the contents of /mnt/glusterfs/salsoman/output/FS/fsaverage/label/lh.BA1.label?
I've attached our current one so that you can compare
cheers Bruce On Tue, 25 Jun 2013, Salil Soman wrote:
Thank you Doug,
Here are the file contents.
-Sal
Sun Jun 23 22:25:24 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS /mnt/glusterfs/salsoman/freesurfer/bin/recon-all -i SPGR/2536_21_1.nii.gz -s GK_2536_FS -nuintensitycor-3T -nocanorm -openmp 50 -all subjid GK_2536_FS setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer Actual FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18 16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 772831 maxlocks unlimited maxsignal 772831 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buffers cachedMem: 99005808 49579412 49426396 0 1598396 37801604 -/+ buffers/cache: 10179412 88826396 Swap: 10485756 459696 10026060
######################################## program versions used $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:24-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 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_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 50 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:29-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:32-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:33-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:34-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:35-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/24-05:25:36-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: salsoman Machine: barley13.stanford.edu Platform: Linux PlatformVersion: 3.2.0-33-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /mnt/glusterfs/salsoman/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /mnt/glusterfs/salsoman/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /mnt/glusterfs/salsoman/output/FS/GK_2536_FS
mri_convert /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz
mri_convert /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/glusterfs/salsoman/SRC/GK_2536/SPGR/2536_21_1.nii.gz... TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jun 23 22:25:47 PDT 2013 Found 1 runs /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig/001.mgz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS
mri_convert /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz --conform
mri_convert /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/rawavg.mgz... TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) Original Data has (0.8594, 0.8594, 1) mm size and (256, 256, 156) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach.xfm /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Jun 23 22:26:10 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Sun Jun 23 22:38:56 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6134, pval=0.2817 >= threshold=0.0050)
awk -f /mnt/glusterfs/salsoman/freesurfer/bin/extract_talairach_avi_QA.awk/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach_avi.l og
tal_QC_AZS/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach_avi.l og
TalAviQA: 0.97859 z-score: 0 TalAviQA2: 3.3941 #-------------------------------------------- #@# Nu Intensity Correction Sun Jun 23 22:39:05 PDT 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1
/mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri /mnt/glusterfs/salsoman/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux barley13.stanford.edu 3.2.0-33-generic #52-Ubuntu SMP Thu Oct 18 16:29:15 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux Sun Jun 23 22:39:06 PDT 2013 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.7330 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7330/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.7330/nu0.mnc...
Iteration 1 Sun Jun 23 22:39:17 PDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.7330/nu0.mnc ./tmp.mri_nu_correct.mni.7330/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7330/0/ -iterations 1000 -distance 50 [salsoman@barley13.stanford.edu:/mnt/glusterfs/salsoman/output/FS/GK_2536_F S/mri/] [2013-06-23 22:39:18] running: /mnt/glusterfs/salsoman/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.7330/0/ ./tmp.mri_nu_correct.mni.7330/nu0.mnc ./tmp.mri_nu_correct.mni.7330/nu1.imp
Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Use of ?PATTERN? without explicit operator is deprecated at /mnt/glusterfs/salsoman/freesurfer/mni/bin/sharpen_volume line 153. Processing:................................................................ .Done Number of iterations: 109 CV of field change: 0.000986757 [salsoman@barley13.stanford.edu:/mnt/glusterfs/salsoman/output/FS/GK_2536_F S/mri/] [2013-06-23 22:46:39] running: /mnt/glusterfs/salsoman/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7330/nu0.mnc ./tmp.mri_nu_correct.mni.7330/0//template.mnc
Transformingslices:.................................................................... ..................Done Transformingslices:.................................................................... ........................................................................... ........................................................................... ......................................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7330/ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7330/ones.mgz sysname Linux hostname barley13.stanford.edu machine x86_64 user salsoman
input ./tmp.mri_nu_correct.mni.7330/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.7330/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7330/input.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7330/input.mean.dat sysname Linux hostname barley13.stanford.edu machine x86_64 user salsoman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.7330/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.7330/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7330/output.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7330/ones.mgz --i ./tmp.mri_nu_correct.mni.7330/nu1.mnc --sum ./tmp.mri_nu_correct.mni.7330/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7330/output.mean.dat sysname Linux hostname barley13.stanford.edu machine x86_64 user salsoman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.7330/ones.mgz Loading ./tmp.mri_nu_correct.mni.7330/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.7330/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.7330/nu1.mnc ./tmp.mri_nu_correct.mni.7330/nu1.mnc mul .90527967007596602086 Saving result to './tmp.mri_nu_correct.mni.7330/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.7330/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.7330/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.7330/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping (11, 68) to ( 3, 110)
Sun Jun 23 22:48:17 PDT 2013 mri_nu_correct.mni done
mri_add_xform_to_header -c /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Jun 23 22:48:19 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.097 -0.025 -0.058 1.356; 0.020 1.037 0.488 -12.228; 0.025 -0.377 1.099 4.862; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times
3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 76 (76), valley at 58 (58) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 76 (76), valley at 58 (58) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 4 minutes and 10 seconds. #-------------------------------------------- #@# Skull Stripping Sun Jun 23 22:52:31 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_em_register -skull nu.mgz /mnt/glusterfs/salsoman/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
======= NUMBER OF OPENMP THREADS = 50 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading'/mnt/glusterfs/salsoman/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.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=15.0 skull bounding box = (49, 48, 35) --> (207, 208, 231) using (102, 101, 133) as brain centroid... mean wm in atlas = 126, using box (83,81,109) --> (121, 120,157) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 initial log_p = -4.8
First Search limited to translation only.
max log p = -4.714732 @ (-9.091, -9.091, -27.273) max log p = -4.622298 @ (13.636, -4.545, 4.545) max log p = -4.568388 @ (-2.273, -2.273, 2.273) max log p = -4.567887 @ (-3.409, 1.136, -1.136) max log p = -4.554366 @ (-0.568, -5.114, 0.568) max log p = -4.554366 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -19.9, -21.0): log p = -4.554
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.6 (thresh=-4.5) 1.064 0.000 0.000 -9.830; 0.000 1.194 0.320 -71.787; 0.000 -0.320 1.194 -0.574; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.000 0.000 -9.830; 0.000 1.270 0.340 -84.084; 0.000 -0.296 1.105 7.422; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 2 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.000 0.000 -9.830; 0.000 1.270 0.340 -84.084; 0.000 -0.296 1.105 7.422; 0.000 0.000 0.000 1.000; reducing scale to 0.2500
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.082 -0.052 0.020 -7.974; 0.036 1.306 0.390 -99.503; -0.033 -0.327 1.073 19.471; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 4 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.082 -0.052 0.020 -7.974; 0.036 1.306 0.390 -99.503; -0.033 -0.327 1.073 19.471; 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=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.084 -0.052 0.020 -8.295; 0.035 1.296 0.416 -101.760; -0.034 -0.358 1.062 25.483; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.084 -0.052 0.020 -8.295; 0.035 1.296 0.416 -101.760; -0.034 -0.358 1.062 25.483; 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 1.08441 -0.05186 0.02026 -8.29545; 0.03508 1.29640 0.41613 -101.75975; -0.03396 -0.35825 1.06199 25.48265; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08441 -0.05186 0.02026 -8.29545; 0.03508 1.29640 0.41613 -101.75975; -0.03396 -0.35825 1.06199 25.48265; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.084 -0.052 0.020 -8.295; 0.035 1.296 0.416 -101.760; -0.034 -0.358 1.062 25.483; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -4.1 (old=-4.8) transform before final EM align: 1.084 -0.052 0.020 -8.295; 0.035 1.296 0.416 -101.760; -0.034 -0.358 1.062 25.483; 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 1.08441 -0.05186 0.02026 -8.29545; 0.03508 1.29640 0.41613 -101.75975; -0.03396 -0.35825 1.06199 25.48265; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08441 -0.05186 0.02026 -8.29545; 0.03508 1.29640 0.41613 -101.75975; -0.03396 -0.35825 1.06199 25.48265; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.084 -0.052 0.020 -8.295; 0.035 1.296 0.416 -101.760; -0.034 -0.358 1.062 25.483; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta... registration took 69 minutes and 47 seconds.
mri_watershed -T1 -brain_atlas /mnt/glusterfs/salsoman/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details)
The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed
*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=122 z=125 r=70 first estimation of the main basin volume: 1445912 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=105, y=117, z=92, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze...
main basin size=10816010181 voxels, voxel volume =1.000 = 10816010181 mmm3 = 10816010.240 cm3done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=128,y=129, z=122, r=9758iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 45874 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1030067734 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1060864313 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=41 , nb = -1082494987 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1100073048 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=24 , nb = 1081747772
CSF_MAX TRANSITION GM_MIN GM GLOBALbefore analyzing : 32, 43, 52, 73 after analyzing : 32, 49, 52, 55 RIGHT_CER before analyzing : 14, 19, 40, 85 after analyzing : 14, 33, 40, 46 LEFT_CER before analyzing : 15, 23, 44, 76 after analyzing : 15, 37, 44, 46 RIGHT_BRAIN before analyzing : 41, 48, 52, 74 after analyzing : 41, 50, 52, 56 LEFT_BRAIN before analyzing : 34, 45, 52, 71 after analyzing : 34, 49, 52, 54 OTHER before analyzing : 24, 40, 66, 87 after analyzing : 24, 57, 66, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...60 iterations
*********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 65.084, std = 6.593
No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.44, sigma = 7.78 after rotation: sse = 4.44, sigma = 7.78 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.53, its var is 11.13 before Erosion-Dilatation 3.50% of inacurate vertices after Erosion-Dilatation 4.66% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations
mri_strip_skull: done peeling brainBrain Size = 1439142 voxels, voxel volume = 1.000 mm3 = 1439142 mmm3 = 1439.142 cm3
Saving brainmask.auto.mgz done
cp brainmask.auto.mgz brainmask.mgz
#------------------------------------- #@# EM Registration Mon Jun 24 00:03:10 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
======= NUMBER OF OPENMP THREADS = 50 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/mnt/glusterfs/salsoman/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 = 84.4 (994 zeros)
spacing=8, using 2772 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, 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=25.1 skull bounding box = (61, 67, 54) --> (194, 197, 206) using (105, 110, 130) as brain centroid... mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.3
First Search limited to translation only.
max log p = -4.046112 @ (-9.091, -9.091, -27.273) max log p = -3.926434 @ (4.545, -4.545, 4.545) max log p = -3.926434 @ (0.000, 0.000, 0.000) max log p = -3.911584 @ (3.409, -1.136, -5.682) max log p = -3.897925 @ (-2.841, 2.841, 5.114) max log p = -3.897925 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -11.9, -23.3): log p = -3.898
Nine parameter search. iteration 0 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 (thresh=-3.9) 1.064 0.000 0.000 -12.315; 0.000 1.148 0.453 -81.971; 0.000 -0.432 0.988 42.250; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 1 nscales = 0 ...
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.055 -0.150 -0.059 15.090; 0.128 1.052 0.415 -82.117; 0.000 -0.464 1.062 37.519; 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 1.081 -0.059 0.014 -8.838; 0.025 1.116 0.400 -76.717; -0.035 -0.415 1.056 32.599; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 3 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.101 -0.061 0.014 -11.382; 0.025 1.116 0.400 -78.592; -0.034 -0.407 1.036 33.963; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 4 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.098 -0.079 0.007 -7.337; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 5 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached
Computing MAP estimate using 2772 samples...
dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10052 -0.07872 0.00715 -7.65093; 0.04280 1.10969 0.41752 -81.72749; -0.03428 -0.42408 1.02550 37.91086; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10052 -0.07872 0.00715 -7.65093; 0.04280 1.10969 0.41752 -81.72749; -0.03428 -0.42408 1.02550 37.91086; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -3.3 (old=-4.3) transform before final EM align: 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000;
EM alignment process ... Computing final MAP estimate using 312841 samples.
dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10052 -0.07872 0.00715 -7.65093; 0.04280 1.10969 0.41752 -81.72749; -0.03428 -0.42408 1.02550 37.91086; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10052 -0.07872 0.00715 -7.65093; 0.04280 1.10969 0.41752 -81.72749; -0.03428 -0.42408 1.02550 37.91086; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach.lta... registration took 56 minutes and 24 seconds. #-------------------------------------- #@# CA Normalize Mon Jun 24 00:59:34 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/mnt/glusterfs/salsoman/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=25.1 skull bounding box = (61, 67, 54) --> (194, 197, 206) using (105, 110, 130) as brain centroid... mean wm in atlas = 107, using box (89,94,111) --> (121, 125,148) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.101 -0.079 0.007 -7.651; 0.043 1.110 0.418 -81.727; -0.034 -0.424 1.025 37.911; 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 (129, 73, 57) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0 0 of 209 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 73, 57) --> (130, 171, 203) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 230.0 0 of 240 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 151, 89) --> (179, 188, 135) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 230.0 1 of 12 (8.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (92, 151, 85) --> (133, 189, 136) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 230.0 0 of 15 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 139, 115) --> (147, 197, 144) Brain_Stem: limiting intensities to 90.0 --> 230.0 0 of 9 (0.0%) samples deleted using 485 total control points for intensity normalization... bias field = 1.019 +- 0.065 1 of 484 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 73, 57) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0 0 of 250 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 73, 57) --> (130, 171, 203) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 233.0 0 of 268 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 151, 89) --> (179, 188, 135) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 233.0 0 of 60 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (92, 151, 85) --> (133, 189, 136) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 233.0 0 of 62 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 139, 115) --> (147, 197, 144) Brain_Stem: limiting intensities to 75.0 --> 233.0 0 of 79 (0.0%) samples deleted using 719 total control points for intensity normalization... bias field = 1.010 +- 0.067 0 of 719 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 73, 57) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 238.0 0 of 301 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 73, 57) --> (130, 171, 203) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 238.0 0 of 377 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 151, 89) --> (179, 188, 135) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0 0 of 82 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (92, 151, 85) --> (133, 189, 136) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 238.0 0 of 65 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 139, 115) --> (147, 197, 144) Brain_Stem: limiting intensities to 73.0 --> 238.0 0 of 147 (0.0%) samples deleted using 972 total control points for intensity normalization... bias field = 1.007 +- 0.053 2 of 972 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 55 seconds. #-------------------------------------- #@# CA Reg Mon Jun 24 01:02:30 PDT 2013 /mnt/glusterfs/salsoman/output/FS/GK_2536_FS/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /mnt/glusterfs/salsoman/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
======= NUMBER OF OPENMP THREADS = 50 ======= reading input volume 'norm.mgz'... reading GCA '/mnt/glusterfs/salsoman/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.45 (predicted orig area = 5.5) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=96777 0001: dt=129.472000, rms=0.728 (9.599%), neg=0, invalid=96777 0002: dt=92.480000, rms=0.712 (2.226%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.699 (1.800%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.693 (0.860%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.687 (0.887%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.684 (0.413%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.680 (0.585%), neg=0, invalid=96777 0008: dt=110.976000, rms=0.679 (0.242%), neg=0, invalid=96777 0009: dt=110.976000, rms=0.676 (0.391%), neg=0, invalid=96777 0010: dt=110.976000, rms=0.673 (0.464%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.669 (0.563%), neg=0, invalid=96777 0012: dt=110.976000, rms=0.666 (0.489%), neg=0, invalid=96777 0013: dt=110.976000, rms=0.661 (0.684%), neg=0, invalid=96777 0014: dt=110.976000, rms=0.658 (0.493%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.655 (0.439%), neg=0, invalid=96777 0016: dt=110.976000, rms=0.653 (0.321%), neg=0, invalid=96777 0017: dt=110.976000, rms=0.651 (0.311%), neg=0, invalid=96777 0018: dt=110.976000, rms=0.649 (0.263%), neg=0, invalid=96777 0019: dt=110.976000, rms=0.648 (0.202%), neg=0, invalid=96777 0020: dt=110.976000, rms=0.647 (0.218%), neg=0, invalid=96777 0021: dt=110.976000, rms=0.646 (0.148%), neg=0, invalid=96777 0022: dt=110.976000, rms=0.644 (0.166%), neg=0, invalid=96777 0023: dt=110.976000, rms=0.644 (0.139%), neg=0, invalid=96777 0024: dt=110.976000, rms=0.642 (0.173%), neg=0, invalid=96777 0025: dt=110.976000, rms=0.641 (0.153%), neg=0, invalid=96777 0026: dt=110.976000, rms=0.640 (0.164%), neg=0, invalid=96777 0027: dt=110.976000, rms=0.640 (0.146%), neg=0, invalid=96777 0028: dt=110.976000, rms=0.639 (0.135%), neg=0, invalid=96777 0029: dt=110.976000, rms=0.638 (0.119%), neg=0, invalid=96777 0030: dt=110.976000, rms=0.637 (0.137%), neg=0, invalid=96777 0031: dt=110.976000, rms=0.636 (0.126%), neg=0, invalid=96777 0032: dt=110.976000, rms=0.636 (0.090%), neg=0, invalid=96777 0033: dt=110.976000, rms=0.635 (0.063%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.635 (0.051%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.635 (0.000%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.635 (0.030%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.634 (0.062%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.634 (0.034%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.634 (0.027%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0040: dt=295.936000, rms=0.632 (0.322%), neg=0, invalid=96777