Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

Correcting left-right flip for multiple subjects at the same timepoint
by Chiu, Bryan (PHTH) 23 Jun '14

23 Jun '14

Hi, I'm attempting to do some longitudinal processing on a set of data with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months after Final. When visually checking over a subject in Freeview, I notice that all of my Midpoint runs are left-right flipped, where the other 3 timepoints' scans are congruent with one another. What can I do to flip these Midpoint volumes left-right before I rerun them all in recon-all "-all"? As well, since these are going to the same subjects for my longitudinal design in creating a 'base' file we have to ensure that we maintain the same orientation of the brain across all timepoints (left-right)? Thanks in advance, - Bryan

2 1

Retinotopic mapping using selxavg3-sess
by Alan Lee 23 Jun '14

23 Jun '14

Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 33333): selxavg3-sess -a Retinotopy.33333.lh -s 33333 I got the following message: "ERROR: /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does not exist" It seems to look for a Retintopy folder within /Retinotopy/33333/. I suppose the Retinotopy folder should be placed under freesurfer/subjects/ ? Am I missing something here? Any help would be greatly appreciated. Many thanks, Alan ===================== debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess -a Retinotopy.33333.lh -s 33333 Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.33333.lh-140617154401.log -------------------------------------------------------------- preproc-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.33333.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ root setenv FREESURFER_HOME /usr/local/freesurfer/ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/Structural Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux /usr/local/freesurfer/subjects/Retinotopy /usr/local/freesurfer//fsfast/bin/preproc-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.33333.lh -nolog Tue Jun 17 15:44:05 CEST 2014 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain 33333 Template ----------------------------- mktemplate-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -fsd Retinotopy -nolog -update Session: /usr/local/freesurfer/subjects/Retinotopy/33333 ---------------- Tue Jun 17 15:44:06 CEST 2014 ERROR: /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does not exist ===================== -- Alan Lee sites.google.com/site/alanlflee/

3 7

recon-all ERROR, no idea why
by Remy Wahnoun 23 Jun '14

23 Jun '14

hello, freesurfers, Im having trouble using recon-all, I tried the prebuilt virtual machine and a fresh unbuntu install without luck. Would anyone have a look at my recon-all.log? I cant spot any error. *Thanks * *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net <http://www.NeuralControl.net>* Mon Jun 23 11:35:42 EDT 2014 /media/sf_Imagery/FreeSurfer/xx /usr/local/freesurfer/bin/recon-all -i /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img00001.dcm -subjid xx -sd /media/sf_Imagery/FreeSurfer -all subjid xx setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28136 maxlocks unlimited maxsignal 28136 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3616064 692400 2923664 0 94528 405020 -/+ buffers/cache: 192852 3423212 Swap: 1944572 0 1944572 ######################################## 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: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 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: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:42-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:43-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/23-15:35:44-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-64-generic CompilerName: GCC CompilerVersion: 30400 ####################################### 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 ####################################### /media/sf_Imagery/FreeSurfer/xx mri_convert /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img00001.dcm /media/sf_Imagery/FreeSurfer/xx/mri/orig/001.mgz mri_convert /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img00001.dcm /media/sf_Imagery/FreeSurfer/xx/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img00001.dcm... Starting DICOMRead2() dcmfile = /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img00001.dcm dcmdir = /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110) Ref Series No = 601 Found 112 files, checking for dicoms Found 110 dicom files in series. First Sorting Computing Slice Direction Vs: 0.0888448 -0.325504 1.15159 Vs: 0.0740373 -0.271253 0.959656 Second Sorting Counting frames nframes = 1 nslices = 110 ndcmfiles = 110 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.2-- Loading pixel data TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 i_ras = (-0.995951, -0.069321, -0.0572432) j_ras = (0.0509968, -0.960008, 0.275289) k_ras = (-0.0740373, 0.271253, 0.959656) writing to /media/sf_Imagery/FreeSurfer/xx/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jun 23 11:37:54 EDT 2014 Found 1 runs /media/sf_Imagery/FreeSurfer/xx/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 /media/sf_Imagery/FreeSurfer/xx/mri/orig/001.mgz /media/sf_Imagery/FreeSurfer/xx/mri/rawavg.mgz /media/sf_Imagery/FreeSurfer/xx mri_convert /media/sf_Imagery/FreeSurfer/xx/mri/rawavg.mgz /media/sf_Imagery/FreeSurfer/xx/mri/orig.mgz --conform mri_convert /media/sf_Imagery/FreeSurfer/xx/mri/rawavg.mgz /media/sf_Imagery/FreeSurfer/xx/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_Imagery/FreeSurfer/xx/mri/rawavg.mgz... TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 i_ras = (-0.995951, -0.069321, -0.0572432) j_ras = (0.0509968, -0.960008, 0.275289) k_ras = (-0.0740373, 0.271253, 0.959656) Original Data has (0.598958, 0.598958, 1.2) mm size and (384, 384, 110) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_Imagery/FreeSurfer/xx/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_Imagery/FreeSurfer/xx/mri/transforms/talairach.xfm /media/sf_Imagery/FreeSurfer/xx/mri/orig.mgz /media/sf_Imagery/FreeSurfer/xx/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jun 23 11:38:06 EDT 2014 /media/sf_Imagery/FreeSurfer/xx/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux recon-all -s xx exited with ERRORS at Mon Jun 23 11:38:10 EDT 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

Re: [Freesurfer] Why the result was not same for the same subject
by wangkangcheng_gmail 23 Jun '14

23 Jun '14

Dear Bruce Yes. The following is an example result for the subject (The id from Sub_1 to Sub_10 is the same subject) that I calculate ten times. rh.aparc.a2009s.volume rh_G_and_S_frontomargin_volume Sub_1 1713 Sub_2 1950 Sub_3 1789 Sub_4 1783 Sub_5 1879 Sub_6 1778 Sub_7 1892 Sub_8 1782 Sub_9 1799 Sub_10 1799 Thank you Wang Kangcheng

2 1

Re: [Freesurfer] problem of Label file
by wangkangcheng_gmail 23 Jun '14

23 Jun '14

Dear Bruce, The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right? Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China

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Vertex analysis cluster values
by Rachel Jonas 23 Jun '14

23 Jun '14

Hi Freesurfer users, I ran a GLM vertex analysis testing an interaction between group and a task measure, and a few clusters popped up that survived correction. I extracted the mean thickness values at the clusters (using cache.th13.abs.y.ocn.dat) in order to plot these interactions in graph form. When I did this, the interactions look nonexistent, and there doesn't appear to be any relationships between my task measure and thickness in either group. My FSGD file contains 4 groups (patients & controls with two different scanner sites), and my continuous variables are age and this task measure. I only have 15 patients and 15 controls, so my only thought so far is that my power is low, and these results are spurious. My contrast file is: 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 Any insight would be greatly appreciated! Thank you! Rachel

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How to extract significant result for each subject
by kangchengwang0808＠gmail.com 23 Jun '14

23 Jun '14

Dear freesurfers, I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this? Thank you Wang Kangcheng ( New learner of freesurfer )

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Labels to annotation
by Karen Marie Sandø Ambrosen 23 Jun '14

23 Jun '14

Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen

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Project probabilistic connectivity maps to pial and calculate mass center
by gong jinnan 23 Jun '14

23 Jun '14

Dear all, I have used probabilistic tractography methods by FSL-FDT to get probabilistic connectivity between grey-white matter interface of precentral and basal ganglia in subjects’ space. The latter one was used as classification mask. And then all of tractography maps were registered to MNI space. Now I want to project tractography results like seed_to_BG.nii.gz to pial in Freesurfer and calculate mass center of those maps. But unfortunately I am not clear how to do that. So there is my question: 1.It is not difficult to project seed_to_BG.nii.gz to .../mri/orig.mgz. But how to project to pial after that? 2.How can I get mass center like pictures in attachment. I tried calculated mass center of seed_to_BG.nii.gz in MNI space, but the mass center point does not fall in precentral. So I want to do that in pial. 3.How to transform subjects’ pial to talairach pial? I searched method to do that for a long time, but have no idea yet. So I hope I can get valuable suggestions here. I will be grateful if you can help me! Sincerely， Jinnan Gong Best wishes for you! Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China

2 1

Group analysis over different studies?
by Terri Scott 23 Jun '14

23 Jun '14

Hi all, I want to do a group analysis using subjects that were run in different studies but who have (some of) the same relevant functional contrasts. Is there a way to run something like isxconcat-sess on data from different analysis streams? Or if not, which files do I need to collect and align from each subject in order to run mri_glmfit? What would be the best way to handle this analysis? Thanks, Terri

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Freesurfer June 2014