Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Freesurfer 5.3 error
by Salil Soman 25 Jun '13

25 Jun '13

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(a)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 cached >> Mem: 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 cm3 >> done. >> 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=9758 >> iterations >> ^^^^^^^^ 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 >> GLOBAL >> before 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 brain >> >> Brain 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 > >

2 1

Freesurfer 5.3 error
by Salil Soman 25 Jun '13

25 Jun '13

Dear Freesurfer experts, I had been running freesurfer 5.3 without trouble on a sungrid cluster of ubuntu servers. Recently, however, I am now getting a new error: Loading source label. Invalid argument ERROR reading /mnt/glusterfs/salsoman/output/FS/fsaverage/label/lh.BA1.label 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 recon-all -s GK_2536_FS exited with ERRORS at Mon Jun 24 13:55:21 PDT 2013 Any suggestions on how I can fix this problem would be a great help. The log file is attached. Best wishes, Sal

2 1

Difficulty Visualizing Hippo-Subfields
by Mike Strupp-Levitsky 25 Jun '13

25 Jun '13

Hi All, I'm having a problem related to that of Ed Gronensch (see below) with viewing the hippocampal subfields overlaid on the nu.mgz mri in Freeview. I recently installed the most recent version for FreeSurfer (lion for MAC). When I use the command listed on the website ( cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt) It says in the command console history "Can not find index for color name posterior_left_CA1". When I manually load the subfields through the GUI (by loading them as subsequent volumes), they load just fine, however there is no suitable color pallet this way because the subfield.mgz files are, as you know probabilistic and therefore even when I choose the Lookup Table color map, are shown in rainbow colors. It is clear that these colors are a reflection of the fact that the subfields are probabilistic, not labels. In other words, the value of the image varies on the 0-255 scale and the colors reflect these, rather than the subfields being different discrete colors due to all being part of a mask or something like that. I hope this makes sense. Any help you could provide would be incredibly appreciated. Thanks SO much. Best, Mike ----------------------------------------------------------------------- Mike Strupp-Levitsky, BA Data Manager & Image Analyst Molecular Imaging & Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 212-543-5016 (C): 607-227-8811 Email: ms4637(a)columbia.edu

1 0

Re: [Freesurfer] A segmentation estimation?
by Bruce Fischl 25 Jun '13

25 Jun '13

for the aseg it's these lines: . . . pass 1: 89966 changed. image ll: -2.224, PF=1.000 pass 2: 15019 changed. image ll: -2.221, PF=1.000 pass 3: 5116 changed. pass 4: 2124 changed. writing labeled volume to aseg.auto_noCCseg.mgz... although I guess I only compute it for the first couple of iterations of ICM cheers Bruce On Tue, 25 Jun 2013, Dov Sadan wrote: > This ?Computing Initial Surface Statistics > -face loglikelihood: -8.0702 (-4.0351) > -vertex loglikelihood: -6.6450 (-3.3225) > -normal dot loglikelihood: -3.4961 (-3.4961) > -quad curv loglikelihood: -6.1619 (-3.0810) > Total Loglikelihood : -24.3732 > > > > On Tue, Jun 25, 2013 at 10:34 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > No, not that. That is the density reestimation. Later on it > should write out the log posterior > > > > On Jun 25, 2013, at 3:32 PM, Dov Sadan <dov.sadan.19(a)gmail.com> wrote: > > Dear Buche, > Thank you very much for your quick reply. > > Do you mean those lines: (from recon-all. log) > ================== > . > . > . > gca peak = 0.27536 (62) > mri peak = 0.11940 (97) > Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, > overlap=0.000) > Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, > peak = 96), gca=96.1 > . > . > > =================== > > If this is what you meant, can you shed some light on this log. > What "gca peak" / "mri peak" means? And what the number > insight the parentheses represent ? > > Thanks in advance, > Assaf > > > > > On Tue, Jun 25, 2013 at 9:49 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Dov > > I think it writes out the log posterior at each > iteration of the aseg (mri_ca_label) > > cheers > Bruce > On Tue, 25 Jun 2013, Dov Sadan wrote: > > Hi there, > > I'm wondering if there's any parameter > which can assess the correctness of > the freesurfer's segmentation ( > the aparc.a2009s+aseg.mgz file). > > --> Assuming the freesurfer's algorithm > fitting/minimizing an objective > function, right ? If so, where I can > find the value of this > fitted function ? (or RMS value ?) > > Thanks in advance, > Dov > > > > > The information in this e-mail is intended only for the > person to whom it is > addressed. If you believe this e-mail was sent to you in > error and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact > the sender and properly > dispose of the e-mail. > > > > >

2 2

A segmentation estimation?
by Dov Sadan 25 Jun '13

25 Jun '13

Hi there, I'm wondering if there's any parameter which can assess the correctness of the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file). --> Assuming the freesurfer's algorithm fitting/minimizing an objective function, right ? If so, where I can find the value of this fitted function ? (or RMS value ?) Thanks in advance, Dov

2 4

Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh
by Yang, Zoe 25 Jun '13

25 Jun '13

Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html) We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt Is there anything else that we are missing and should run? Thanks!

3 5

Must have compute capability 2 for GCAMORPH_ON_GPU CUDA device
by Clive Wong 25 Jun '13

25 Jun '13

Dear experts, I'm new to CUDA. I tried to use CUDA in my environment, it gives the message below: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.0 Runtime : 5.0 Acquiring CUDA device Using default device Must have compute capability 2 for GCAMORPH_ON_GPU CUDA device: Quadro NVS 420 I've checked that the Quadro NVS400 is of compute capability 1.1. and the script devicemanagement.c has blocked devices below compute capability 2. Is there any workaround to get it work? Or shall I compile the freesurfer from source code? If yes, how could I know how to setup the configuration? Thanks, Clive

2 1

Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 (Douglas Greve)
by Maria Kharitonova 25 Jun '13

25 Jun '13

Hi, sorry I must have missed your response last week. Yes, I'm doing an identical analysis: comparing 2 groups of kids (controls and ADHD) in cortical thickness, controlling for age and demeaned ICV (nuisance). So all the parameters are the same. I'm attaching 3 screen shots: group differences using 5.0 before using Monte Carlo correction (lots of clusters), group differences before correction using 5.3 (few small clusters), and group differences using 5.0 after correction (frontal cluster). there was nothing sig. remaining after correcting for multi. comparisons using 5.3. I'm puzzled about why the differences are so large. I selected DODS in 5.0, so everything should be the same? Thanks! Maria On Tue, Jun 25, 2013 at 12:02 PM, Maria Kharitonova < maria.kharitonova(a)colorado.edu> wrote: > > Hi, sorry I must have missed your response last week. Yes, I'm doing an > identical analysis: comparing 2 groups of kids (controls and ADHD) in > cortical thickness, controlling for age and demeaned ICV (nuisance). So all > the parameters are the same. I'm attaching 3 screen shots: group > differences using 5.0 before using Monte Carlo correction (lots of > clusters), group differences before correction using 5.3 (few small > clusters), and group differences using 5.0 after correction (frontal > cluster). there was nothing sig. remaining after correcting for multi. > comparisons using 5.3. I'm puzzled about why the differences are so large. > I selected DODS in 5.0, so everything should be the same? > > Thanks! > Maria > > ****** > > Message: 10 > Date: Tue, 18 Jun 2013 23:34:10 -0700 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51C150E2.1080604(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Maria, can you elaborate on exactly what you have done? Is the data > the same and you are only changing the version of QDEC? What is the > nature of the difference? Can you send pics or stats? > doug > > > On 6/18/13 6:06 AM, Maria Kharitonova wrote: > > Hi, > > > > I'm learning how to use QDEC and was comparing results that it produces > under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS > or DOSS method of producing a design matrix, while the 5.3 only has DODS. > This suggests that results should be identical (or at least similar) across > versions if I select DODS. However, I'm getting very different results > based on the version I select: complete lack of differences across groups > in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like > to understand where the differences are stemming from -- any ideas? > > > > Thanks in advance! > > Maria > > > > ******************************* > > > > Maria Kharitonova, Ph.D. > > Postdoctoral Research Fellow > > Laboratories of Cognitive Neuroscience > > Boston Children's Hospital > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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IndexError: list index out of range in post-processing of longitudinal data
by Sandra Preissler 25 Jun '13

25 Jun '13

Dear freesurfer users, we wanted to do longitudinal analyses for two different time points. So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepa…) The "Post-Processing Longitudinal Data" step does not work. (long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage ) After starting the process we get the following error message: Parsing the qdec table: ./qdec/long.qdec.table.dat Traceback (most recent call last): File "/opt/freesurfer/bin/long_mris_slopes", line 521, in <module> qdectable = LongQdecTable(options.qdec) File "/srv/freesurfer/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/srv/freesurfer/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range Weve already tried a lot of things, like removing subjects from the longitudinal qdec table, except for one subject, or deleting every command that was optional, but it still does not work. The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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freesurfer registration
by Parker, Christopher 25 Jun '13

25 Jun '13

Hi, I understand that the recon-all script registers and then averages two anatomical images (after bias field correction) if two are provided in the "orig" folder, before performing the other parcellation stages. I am writing a report and it might be good to mentioned what registration is used. I'm guessing this is a rigid registration using sum of squared differences cost function? Best, Chris

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