Freesurfer

freesurfer@nmr.mgh.harvard.edu

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recon-all exited with erros
by Salem Hannoun 19 Jul '16

19 Jul '16

Hi I’m trying to run free surfer on a set of T1 images. I tried to do it on one patient first before running it on the whole dataset. I ran the recon-all with the -all option I had an error message one minute after it has been launched. It stopped at the mri_nu_correct.mni. Could you please advise on how to fix this error? Please find below the log file Thank you for you help Best regards Salem _____________________________________________ Fri Jul 15 10:20:05 EEST 2016 /usr/local/freesurfer/subjects/AZH /usr/local/freesurfer/bin/recon-all -subject AZH -i AZH.nii -all subjid AZH setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux F23 4.2.3-300.fc23.x86_64 #1 SMP Mon Oct 5 15:42:54 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 31792 maxlocks unlimited maxsignal 31792 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8159752 5185268 174908 7672 2799576 2803616 Swap: 15359996 15359964 32 ######################################## 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: 2016/07/15-07:20:06-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.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: 2016/07/15-07:20:06-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.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: 2016/07/15-07:20:06-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:06-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:06-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:07-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:08-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:09-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:10-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.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: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.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: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/15-07:20:11-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: root Machine: F23 Platform: Linux PlatformVersion: 4.2.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/AZH mri_convert /home/sh156/Desktop/AZH.nii /usr/local/freesurfer/subjects/AZH/mri/orig/001.mgz mri_convert /home/sh156/Desktop/AZH.nii /usr/local/freesurfer/subjects/AZH/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sh156/Desktop/AZH.nii... TR=8.39, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.994667, 0.103136, 0) j_ras = (-0.0980387, 0.945506, -0.310494) k_ras = (-0.0320231, 0.308838, 0.950575) writing to /usr/local/freesurfer/subjects/AZH/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Jul 15 10:20:16 EEST 2016 Found 1 runs /usr/local/freesurfer/subjects/AZH/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 /usr/local/freesurfer/subjects/AZH/mri/orig/001.mgz /usr/local/freesurfer/subjects/AZH/mri/rawavg.mgz /usr/local/freesurfer/subjects/AZH mri_convert /usr/local/freesurfer/subjects/AZH/mri/rawavg.mgz /usr/local/freesurfer/subjects/AZH/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/AZH/mri/rawavg.mgz /usr/local/freesurfer/subjects/AZH/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/AZH/mri/rawavg.mgz... TR=8.39, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.994667, 0.103136, 0) j_ras = (-0.0980387, 0.945506, -0.310494) k_ras = (-0.0320231, 0.308838, 0.950575) Original Data has (1.00001, 0.892857, 0.892857) mm size and (159, 166, 204) 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 /usr/local/freesurfer/subjects/AZH/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/AZH/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/AZH/mri/orig.mgz /usr/local/freesurfer/subjects/AZH/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Jul 15 10:20:28 EEST 2016 /usr/local/freesurfer/subjects/AZH/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux F23 4.2.3-300.fc23.x86_64 #1 SMP Mon Oct 5 15:42:54 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AZH exited with ERRORS at Fri Jul 15 10:20:32 EEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

3 analyses questions
by Caroline Beelen 19 Jul '16

19 Jul '16

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on aparc.stats tables (my ROI's are few regions from DK-atlas). I tried to do the Monte Carlo simulation but get an error that a masking-file is missing. In general, how could I correct for multiple comparisons when using aparcstats2tables in GLM? Alternatively I performed the analysis in Qdec (excluding a nuisance factor to be able to do so). I tried to implement few ROI's from DK-atlas, one at a time, such as left fusiform area. However, when running the analysis it seems to take into account the whole area of the brain and investigates its correlation with a particular selected ROI (i.e. left fusiform area). Would this kind of analysis give me the same results as when only performing stats on this particular region? Actually, for my analysis I'm only interested in few regions of DK-atlas and, if possible, would like to perform it on only these regions, leaving out all of the rest (I'm correcting for ICV anyways). In that case I would also have to correct for fewer multiple comparisons... How could I achieve this in Qdec and/or command-line GLM? Thanks in advance for your help. Regards, Caroline

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Re: [Freesurfer] question about voxel size
by Falk Lüsebrink 19 Jul '16

19 Jul '16

Hi Dorsa, well visual inspection is always a good indicator. Also you could have a look at the QA Tools (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools) I haven’t tested them though. Other than that, I wouldn’t know of any objective method to validate your results. Probably someone else can jump in on that. Best, Falk P.S. Be sure to also reply to the list also. Von: Dorsa Haji Ghaffari [mailto:ghdor@umich.edu] Gesendet: Dienstag, 19. Juli 2016 18:21 An: Falk Lüsebrink Betreff: Re: [Freesurfer] question about voxel size Thank you. I was actually able to get results using my high resolution images without changing their resolution. Is there any way to validate my results to see if I have good results? On Tue, Jul 19, 2016 at 12:10 PM, Falk Lüsebrink <falk.luesebrink(a)ovgu.de<mailto:falk.luesebrink@ovgu.de>> wrote: Hi Dorsa, until version 6 of FreeSurfer is released you could try to follow the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) which should enable you to process the data in its native resolution. With FreeSurfer v6 this workaround will not be necessary anymore, as the processing pipeline has been updated. If you want to, you could also try out a recent developer build. However, it is still under development. Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] Im Auftrag von Dorsa Haji Ghaffari Gesendet: Dienstag, 19. Juli 2016 18:06 An: Freesurfer support list Betreff: [Freesurfer] question about voxel size Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari

1 0

Re: [Freesurfer] Bug in Freesurfer Installation
by Sherryse Corrow 19 Jul '16

19 Jul '16

Of course. I should have known. That fixed the problem. Thank you very much Aman and Z.K. Best, Sherryse

1 0

can not find module 'dev'
by Yun Wang 19 Jul '16

19 Jul '16

Dear All, I recently tried to gain access the read-only CVS source-code repository, however, I have this kind of error: cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules anyone have idea what is going on here? Thank you so much! Best, Yun Wang

2 1

Bug in Freesurfer Installation
by Sherryse Corrow 19 Jul '16

19 Jul '16

Hello freesurfer developers, I installed FreeSurfer on my computer today using the instructions found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. After installation, I proceed to the “test your FreeSurfer Installation” section. Upon trying the first test, I ran the following and code and received the following error. Sherryses-iMac:~ sherrysecorrow$ cd $FREESURFER_HOME/subjects Sherryses-iMac:subjects sherrysecorrow$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz I’ve searched the list and was unable to find someone with the same error in the archives. Any thoughts on how to fix this? freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac OS X version 10.9.5 uname -a Darwin Sherryses-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 Thanks, Sherryse

2 1

T2 vs. T2-FLAIR update
by Michelle T Kassel 19 Jul '16

19 Jul '16

Hello, I am beginning a new study and would like to determine the optimal T2 acquisition parameters for improved pial surface results from FreeSurfer. I am wondering if there is a difference in using a T2 or T2-FLAIR. I have found a discussion post from 2014 which provided useful information (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039580.html) however, it seems from reading the post that newer developments were underway, and I was wondering if I could get an updated answer to the question: is there any difference from freesurfer's perspective of using T2-space or T2-space-flair? Thank you for your help! Michelle

4 3

Request for new mri_tessellate (error: max vertices 1000000 exceeded)
by Ferguson, B. 19 Jul '16

19 Jul '16

Dear Freesurfer team, I am running Falk Luesebrinks hires recon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>, and am running into the error of "mri_tessellate: max vertices 1000000 exceeded" when I run the command line "recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT" on a 0.5mm T1 structural volume. I have seen an earlier e-mail conversation<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42045.html>, and would like to request: is a similar mri_tesselate that is easier about the number of vertices available for my platform? FREESURFER_HOME = /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac version: OS X Yosemite 10.10.5 Kernel info: Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 Thanks in advance, best wishes, Bart Ferguson PhD candidate | Department of Psychiatry | Brain Division | University Medical Center Utrecht Post: A01.126 kantoortuin 1 | Visit: A01.504| Heidelberglaan 100 | 3584 CG UTRECHT T +31 (0)88 75 555 55 | M +31 (0)6 1191 6897 | www.umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

2 1

DeMean Flag
by Clara Kühn 19 Jul '16

19 Jul '16

Dear Freesurfer experts, is there an explanation somewhere for the DeMeanFlag? I can't find it in the wiki but I would like to use it to demean my covariates for the GLM and LME. Cheers Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

2 2

mri_segstats
by Alshikho, Mohamad J. 18 Jul '16

18 Jul '16

Dear FS experts, I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean PET signal for every parcellate and segment in the atlas "wmparc.mgz". Which one of the following commands is more accurate? 1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum PET.wmparc.stats 2. mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ PET.anat.mgz--in-intensity-name norm --in-intensity-units MR --subject ${subj} --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv Best, Mohamad

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