Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

RAS to voxel transform
by Arman Eshaghi 23 Jun '14

23 Jun '14

Hi, I'm trying to understand the conversion from RAS (freesurfer surface coordinate) to volume space (x, y, and z.. According to Graham Wideman documentation here http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not outdated), Right is negative x, *Anterior is positive z*, and *Superior is positive y*. Just to double check, usign mri_info on a sample T1.mgz in one subject I get this ras to voxel transform: -1 0 0 126.944 0 0 -1 135.16 0 1 0 110.6 0 0 0 1 Assuming we have correctly set the (0, 0, 0), and we can extract R A and S (respectively) coordinates using C++ or Python code it means: Right is negative x, *Anterior is negative z*, and *Superior is positive y* (conflicting coordinates are in vold). Am I missing anything here, or coordinate systems have changed from the probably outdated documentation? Thanks in advance for any input on this rather confusing point. All the best, Arman

2 1

QDEC Error loading the data table
by Mohammed Goryawala 23 Jun '14

23 Jun '14

Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freev… However, when I try to load my data table it returns the error. ---------------------------------------------------- Loading data table /home/pcopy_project/qdec/qdec.table.dat... Number of columns: 5 fsid column: 1 Number of factors: 4 Number of subjects: 57 Reading discrete factor levels from config file /home/pcopy_project/qdec/gender.levels Female Male done. Reading discrete factor levels from config file /home/pcopy_project/qdec/diagnosis.levels Control Disease done. ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column INFO: If 'gender' is a discrete factor, then create a file named 'gender.levels' containing the valid factor names one per line. Error loading the data table. -------------------------------------------------------- As you see I have a 'gender.levels' file in the same directory as the data file and it reads it above. I still get the error. I am new to QDEC and any help would be appreciated. Thank you Mohammed Goryawala, PhD Research Associate Department of Radiology University of Miami Miller School of Medicine

2 2

Re: [Freesurfer] Why the result was not same for the same subject
by Chiu, Bryan (PHTH) 23 Jun '14

23 Jun '14

There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainly suggest reading the paper titled: "Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain" - Bryan

3 2

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

6 13

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

2 1

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 )

2 1

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