Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Correct/best way to find the midthickness surface
by Michael Waskom 11 May '16

11 May '16

Hi Freesurfers, I have seen at least three ways for identifying an intermediate surface between the white and pial surfaces: - Multiply the surface normal vector for each white surface vertex by half of the cortical thickness and add it to each vertex coordinate - Average the white and pial coordinates for each vertex - Use mris_expand, e.g. `mris_expand -thickness lh.smoothwm 0.5 lh.graymid` I have found that these approaches all give similar, but not identical results. Is there a consensus that one approach is best relative to the others? Thanks, Michael

2 1

recon-all error on ubuntu 16.04
by Mads Jensen 11 May '16

11 May '16

Dear FreeSurfer group, I get an error trying to run basic recon-all on a ubuntu 16.04 system. It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below). I have made the symbolic links from the installation notes. Any ideas or thoughts on what the problem might be or how to track it down would be very welcome. best regards, mads from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: stretch/sid Kernel info: Linux 4.4.0-22-generic x86_64 recon-all.log: Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 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 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736 ######################################## 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/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/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.mgz... 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) writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz... 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz... mri_add_xform_to_header -c /home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 4

QDEC - cannot allocate memory
by Marissa Pifer 11 May '16

11 May '16

Hi freesurfers, I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - freesurfer version 5.3. I am looking to analyze T2weighted scans for 27 subjects through the qdec system. I keep getting this error that it cannot allocate memory for the task. I'v been talking with our IT people and they've told me I have more than enough space on the computer, so it must be an issue with the program or how it's set up. This is the error message: *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! Cannot allocate memory Does anyone know what I can do to fix this problem? Thanks, Marissa

3 6

cerebellar surface
by Alexopoulos, Dimitrios 11 May '16

11 May '16

Hi all, Freesurfer generates a volumetric parcellation of the cerebellum, but is there a method to generate the surface reconstruction, or perhaps just a hull surface from freesurfer output. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

4 6

Manual segmentation issues
by Saturne Fox 11 May '16

11 May '16

Dear freesurfer users community, I need your help concerning manual segmentation issues.

2 7

GLM - covariate question
by Pedro Rosa 10 May '16

10 May '16

Dear list, I am running a command line group analysis, and I want to include a covariate that is zero for all subjects in a group, and diverse for all subjects in the second group (medication intake, which is null for all subjects in the control group). This generates a lack of range of that continuous variable within a class (control group), and thus mri_glmfit ends with errors. Is it possible to perform such analysis? Could demeaning procedure work here? If not, how could I "regress out" the effect of such covariate in between-groups thickness/area differences? Many thanks in advance, Pedro.

2 2

Stats for Yeo and Choi Parcellations
by Bronwyn Overs 10 May '16

10 May '16

Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I noticed that the Yeo 2011 annot files are already available in fsaverage/label. How do I map these annot file to each of my subjects so that I can extract stats? 2. For the Choi 2012 files I wish to use Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I map this file to each of my subjects so that I can extract stats for the 7Network parcellation? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

4 9

(no subject)
by Николай Семибратов 10 May '16

10 May '16

Dear experts, I would like to ask you for some advice about matrix. I use FreeSurfer for automatic segmentation of infant brains and have a problem with infants under 6 months. Could you give me advice what are the optimal parameters of the matrix for automatic segmentation from newborns to 6-month-olds? I work on Philips Ingenia 1,5T. T1 3D program runs with the settings ACQ matrix 244x216, TR / TE 7.3 / 3.4. Reconstruction matrix 288, Voxel size 1,05 mm. Any advice would be really appreciated! Best Regards

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 4
by Domenico Zacà 10 May '16

10 May '16

Hi Bruce, thank you for your reply. Indeed that's the way to do it. However how can I automatically build an updated color code scale for the new annotation/label file? The analysis I'm running clusters together the ROIs from the old annotation file based on the network analysis results. I have done it manually because I had only 13 clusters to take care of but I'd prefer to find an automated way if possible also to be consistent if I'm comparing the cluster algorithm results between different groups. Cheers, Domenico Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri On Mon, May 2, 2016 at 8:59 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. no recon button (Burke,Sarah E) > 2. Brainstem segmentation (Haque, Muhammad E) > 3. Re: import ROI analysis results from Matlab into FreeSurfer > (Bruce Fischl) > 4. Re: no recon button (Douglas Greve) > 5. Re: no recon button (Burke,Sarah E) > 6. Re: no recon button (Douglas Greve) > 7. Re: no recon button (Burke,Sarah E) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 May 2016 16:14:28 +0000 > From: "Burke,Sarah E" <saraheburke(a)ufl.edu> > Subject: [Freesurfer] no recon button > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > BLUPR0801MB155544A9C1E2604C95B3B8DCB8790(a)BLUPR0801MB1555.namprd08.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > > I searched the mail list and saw that others have had this problem, but I > see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview > for Linux. I have no recon button. What should I do? > > > Thank you >

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[Vacancy] Postdoc Position to Study Brain and Behavioral Plasticity Occurring with Spaceflight and Analog Environments.
by Vincent Koppelmans 10 May '16

10 May '16

A funded postdoctoral position is available immediately (with start date in summer 2016) to work in Dr. Rachael Seidler’s laboratory at the University of Michigan studying brain and behavioral plasticity occurring with spaceflight and analog environments. As one of the world’s leading research institutions, the University of Michigan provides an exceptionally supportive environment for research. University support includes integrated and state of the art computer technology, exceptional students and staff, and a network of world-renowned scientists. The Neuromotor Behavior Laboratory (directed by Dr. Seidler) is an interdisciplinary, productive, and dynamic group of students and staff researching the neurocognitive control of movement. The post-doctoral researcher will study cognitive, sensory, and motor behavioral plasticity and their neural correlates using functional MRI and resting state connectivity. The candidate will be expected to work collaboratively with a research team to collect and analyze data, prepare manuscripts for publication, and participate at national and international level meetings. The candidate must be willing and able to travel internationally for data collection. Interested applicants should submit a cover letter, curriculum vita, and the names and contact information for two referees to Rachael D. Seidler, Ph.D. via e-mail (rseidler(a)umich.edu <mailto:rseidler@umich.edu>). Review of applications will begin immediately. Necessary Qualifications: Ph.D. in psychology, neuroscience, kinesiology or related field and experience with MRI techniques including structural MRI, DTI, and / or functional MRI. The candidate must possess excellent verbal and written communication skills, be strongly motivated, and work well in a team setting. Experience with computer programming a plus (MATLAB, LabView, and / or E-Prime). The position is initially available for one year and may be renewable. Questions regarding the position can be emailed to rseidler(a)umich.edu <mailto:rseidler@umich.edu>. The University of Michigan is an Equal Opportunity, Affirmative Action Employer.

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