Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

question abt supratentorial vol and total brain vol.
by Ritobrato Datta 24 May '13

24 May '13

Hello All, I am using freesurfer 5.1 for my analysis. I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated. Here are some measures - For 79 subjects - Average Total Brain Vol = 1038395.291 Average SupraTentorialVol = 979996.4684 Is that expected ? Is it possible that CSF vol is part of Total Brain Vol ? Any insight will be helpful. Thanks Rito

2 2

sig.nii.gz
by dgw 24 May '13

24 May '13

Hi, I am trying to compare the quality of fMRI data with different artifact inducing objects in the magnet. I ran expanding and contracting rings and followed the retinotopy fsfast analysis in FreeSurfer 5.1.0. I am trying to compare the data by looking at the sig.nii.gz (which from the website should correspond to the voxel-wise significances) with the different artifacts. I am not sure though how to interpret the negative values for a retinotopy analysis? Can someone clarify what the negative values represent. I would have expected the significance to only be positive, as there isn't a traditional contrast in the smoothly varying stimulus. Thanks! Dan

2 1

mri_concat --conjunct
by Caspar M. Schwiedrzik 24 May '13

24 May '13

Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar

2 7

problem with libreadline.so.5
by Erin W. E. Dickie 24 May '13

24 May '13

Hello, I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Is libreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins. Thank you, Erin Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618 /home/t/tpaus/raleong/freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 20000 memorylocked unlimited maxproc 257772 total used free shared buffers cached Mem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/t/tpaus/raleong/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/t/tpaus/raleong/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618 mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618 mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) 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 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz... mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach.xfm /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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 Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050) awk -f /home/t/tpaus/raleong/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log tal_QC_AZS /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log TalAviQA: 0.97680 z-score: #-------------------------------------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri /home/t/tpaus/raleong/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 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.9181 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/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=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/0/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:00:54] running: /home/t/tpaus/raleong/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9181/0/ ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:05] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/1/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:10] running: /home/t/tpaus/raleong/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9181/1/ ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:20] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz sysname Linux hostname gpc-f146n031 machine x86_64 user edickie input ./tmp.mri_nu_correct.mni.9181/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/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.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/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.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/input.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/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.9181/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/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.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/nu2.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.9181/output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/nu2.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 4

tracula mris_resample: Command not found
by stdp82＠virgilio.it 24 May '13

24 May '13

Hi Anastasia, I'm re-running tracula by using new version 5.3. In the step 3 (trac-all -inter -c $FREESURFER_HOME/configurazion_file) I have this error: MRISregister() return, current seed 0writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 11110: 1 negative trianglesmris_resample: Command not found.Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 I'm attaching the configuration file that I have used. What's happened? Thank you very much, Stefano

2 1

tkmedit BUS error
by Amber M Gregory 24 May '13

24 May '13

I am having a problem using tkmedit and tksurfer with Freesurfer. Freeview is working. Below is the tkmedit error and relevant specs. Any suggestions are welcome. General Specs Apple OS 10.6.8 Processor: 2x 2.26 Ghz Quad-core Intel Xeon 16 GB DDR3 Freesurfer Ver 5.3.0 Chipset Model: NVIDIA GeForce GT 120 Graphic card Specs Chipset Model: NVIDIA GeForce GT 120 Type: GPU Bus: PCIe Slot: Slot-1 PCIe Lane Width: x16 VRAM (Total): 512 MB Vendor: NVIDIA (0x10de) Device ID: 0x0640 Revision ID: 0x00a1 ROM Revision: 3386 Displays: VG930m-3: Resolution: 1280 x 1024 @ 60 Hz Pixel Depth: 32-Bit Color (ARGB8888) Display Serial Number: QC2094821097 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Display Connector: Status: No Display Connected Code [Victor-Marks-Mac-Pro:subjects/bert/mri] victormark% tkmedit bert/ brainmask.mgz -aux T1.mgz -surfs -aseg Couldn't create output file .xdebug_tkmedit^CKilled [Victor-Marks-Mac-Pro:subjects/bert/mri] victormark% cd .. [Victor-Marks-Mac-Pro:freesurfer/subjects/bert] victormark% cd .. [Victor-Marks-Mac-Pro:/Applications/freesurfer/subjects] victormark% tkmedit bert/ brainmask.mgz -aux T1.mgz -surfs -aseg Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. LoadSegmentationVolume main aseg.mgz /Applications/freesurfer//FreeSurferColorLUT.txt Bus error

2 1

'Bus error' when running commands from the "Testing your FreeSurfer Installation" wiki page
by Swartz, Max 24 May '13

24 May '13

Happy Friday! I was able to install FreeSurfer v5.3.0 on my personal Macbook (2.4 GHz Intel Core i5 processor, 4 GB 1067 MHz DDR3, Mac OS X 10.6.8). Unfortunately, I'm still getting some error messages as I run through the commands on the "Testing your FreeSurfer Installation" page in the manual. Originally, I was receiving the following error message when trying to run the "tkmedit" commands (such as "tkmedit bert norm.mgz"): - "dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib" - Followed by "Referenced from: /Applications/freesurfer/tktools/tkmedit.bin Reason: image not found" To remedy the situation, I downloaded and installed XQuartz. Now the error message I receive is simply "Bus error". It also appears when I try to run the "tksurfer" and "qdec" commands as well. I have not yet tried the "recon-all" command. If you have any ideas how I can fix this or any suggestions, I'd really appreciate it. Thanks, and have a great weekend, Max

2 1

FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11
by Swartz, Max 24 May '13

24 May '13

Hello, I am working as a research assistant for the summer with the University of Cincinnati's Psychiatry department in the Division of Bipolar Disorders Research under Cal Adler and Melissa DelBello. We are looking to start utilizing FreeSurfer; however, I am getting some error messages when trying to perform most of the tasks on the "Testing your FreeSurfer installation" page in the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer ). The most common of the error messages I am receiving is "Exec format error. Binary file not executable." The Mac I am trying to run FreeSurfer on has a dual 2 GHz PowerPC G5 processor and 4 GB DDR SDRAM, and is running Mac OS X 10.4.11 (Tiger). I have been trying to use FreeSurfer v5.3.0 for SnowLeopard OS X 10.6 (32b Intel). Should this version compatible with my computer? We are thinking that our error messages are the result of either operating system incompatibility or not having all of the necessary privileges on our account (which can be fixed through IT). Any insight you can provide regarding the compatibility of FreeSurfer v5.3.0 on Mac OS X 10.4 Tiger systems would be incredibly helpful. Thanks so much, Max Swartz

3 3

Bug report: QDEC
by Tudor Popescu 24 May '13

24 May '13

Just reporting a GUI bug in QDEC: after setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so. Hope that helps, Tudor

2 2

p-value visualization
by Ludovici, Katharine (NIH/NIMH) [F] 24 May '13

24 May '13

Hello, We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's? Thanks very much, Katie Ludovici Postbaccalaureate IRTA National Institute of Mental Health Child Psychiatry Branch 301-435-5557

3 3

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