Dear Experts, I save the longitudinal sample data to the path: /usr/local/src/freesurfer/subjects/long-tutorial, then run d4201z-CELSIUS-M470-2:/usr/local/src/freesurfer/subjects/long-tutorial> freeview -v OAS2_0001/mri/norm.mgz ? -f OAS2_0001/surf/lh.pial:edgecolor=red ? OAS2_0001/surf/rh.pial:edgecolor=red ? OAS2_0001/surf/lh.white:edgecolor=blue ? OAS2_0001/surf/rh.white:edgecolor=blue Failed, error message shows: freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Freesurfer version: 5.1, System : ubunto Could you give me hints how to solve the problem? Thanks, Yawu

Hi Yawu, look in the paper by Christophe Destriuex (2010 Neuroimage). It gives a table of all these ROIs doug

On 10/02/2012 02:29 AM, yawu Liu wrote:

Dear Experts, How to know the full name of structures in the output? such as G_Ins_lg_and_S_cent_ins, S_oc-temp_med_and_Lingual... Regards, Yawu

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Hi

I downloaded about Tuesday and this morning. However when I download a bit later to day I got a working mri_segstats.It print out mri_segstats --all-infoProgramName: mri_segstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2012/10/02-19:57:40-GMT BuildTimeStamp: Jun 20 2012 12:45:04 CVS: $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ User: knutjb Machine: dmed4960 Platform: Linux PlatformVersion: 3.2.0-32-generic CompilerName: GCC CompilerVersion: 40100

Best regards Knut J

On 10/02/2012 06:04 PM, Douglas N Greve wrote:

Hi Knut, when did you download mri_segstats? Can you send me the result of mri_segstats --all-info doug

On 10/02/2012 01:42 AM, Knut J Bjuland wrote:

...

I have download the latest verion of mri_segstats from the release notes. But it does not generate asegstats.

4 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012 /home/knutjb/freesurfer/20_ucsd_automatic_version2/004

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv

mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004

ERROR: Option --sum unknown

#------------------------------------------

recon-all -s 004 finished without error at Tue Oct 2 07:36:17 CEST 2012 done

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats USAGE: mri_label2vol

    Possible inputs:
  --label labelid<--label labelid>
  --annot annotfile : surface annotation file
  --seg   segpath : segmentation
  --aparc+aseg  : use aparc+aseg.mgz in subjectdir as seg

  --temp tempvolid : output template volume

  --reg regmat : VolXYZ = R*LabelXYZ
  --regheader volid : label template volume (needed with --label or

--annot) for --seg, use the segmentation volume --identity : set R=I --invertmtx : Invert the registration matrix

  --fillthresh thresh : between 0 and 1 (def 0)
  --labvoxvol voxvol : volume of each label point (def 1mm3)
  --proj type start stop delta

  --subject subjectid : needed with --proj or --annot
  --hemi hemi : needed with --proj or --annot
  --surf surface  : use surface instead of white

  --o volid : output volume
  --hits hitvolid : each frame is nhits for a label
  --label-stat statvol : map the label stats field into the vol
  --stat-thresh thresh : only use label point where stat>  thresh
  --offset k : add k to segmentation numbers (good when 0 should not

be ignored)

  --native-vox2ras : use native vox2ras xform instead of tkregister-style
  --version : print version and exit
  --help

$Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum ERROR: Option --sum unknown

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