Re: [Freesurfer] Problem with mri_segstats

Hi Elizabeth, I'm cc'ing the list so that others may benefit from the answer:

The labels that you are referencing are defined in the aparc.a2009s atlas, but the wmparc is generated from the aparc atlas. To generate a wmparc using the a2009s, run the following:

cd $SUBJECTS_DIR/subject

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz --a2009s

Then reference wmparc.a2009s.mgz instead of wmparc.mgz in the mri_segstats cmd

doug

Elizabeth Gutierrez wrote:

Hi Douglas, Thank you for directing me towards reporting form. Here is more information:

FREESURFER_HOME: /software/Freesurfer/5.0.0

Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-22-generic x86_64

1. subject name - s120 SUBJECTS_DIR - /mindhive/gablab/memory/sourcemem/fsdata_REM

2. the entire command-line executed

*Successful -* mri_segstats --seg /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz --ctab-default --id 3001 --in fa.anat.mgh --sum fa.stats

*Unsuccessful* - mri_segstats --seg /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz --ctab-default --id 3101 --in fa.anat.mgh --sum fa.stats

also unsuccessful for other 30 ids from aparc2009 -id 13112 --id 14112 --id 13113 --id 14113 --id 13114 --id 14114 --id 13118 --id 14118 --id 13115 --id 14115 --id 13116 --id 14116 --id 13123 --id 14123 --id 13137 --id 13138 --id 14138 --id 13148 --id 14148 --id 13150 --id 14150 --id 13163 --id 14163 --id 13153 --id 14153 --id 13154 --id 14154 --id 13155 --id 14155

3. the error message generated Reporting on 0 segmentations

More on fa.stats file :

sysname Linux # hostname ba6 # machine x86_64 # user eguti # anatomy_type volume # # SegVolFile /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz # SegVolFileTimeStamp 2010/06/02 15:09:42 # ColorTable /software/Freesurfer/5.0.0/FreeSurferColorLUT.txt # ColorTableTimeStamp 2010/08/13 20:56:24 # InVolFile fa.anat.mgh # InVolFileTimeStamp 2010/11/05 17:09:14 # InVolFrame 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 1

On Wed, Nov 10, 2010 at 10:45 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Elizabeth,

we'll need more info to track down the problem. Please take a look
at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> for the
kinds of things we need.

thanks

doug
Elizabeth Gutierrez wrote:

    Hi,

    I've been trying to use mri_segstats on a FA map with a white
    matter parcellation file (wmparc.mgz) but there might be a
    problem in the program. When I open the fa.stats output file,
    all the values (std.dev, etc) are 0.0000  for the 2009 table
    parcellation ids. However, when I use the label id 251 (corpus
    collosum) from the first few labels on the list, I get a
    value. When I use the corpus collosum id for more current
    labels like the aparc 2005 and 2009,  I get 0.0000 again.

    Could there be a bug in the program?


    -- 
    Elizabeth C. Gutierrez
    Graduate Student
    Department of Brain and Cognitive Sciences
    Massachusetts Institute of Technology
    ------------------------------------------------------------------------

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



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