Hi Taylor,

for plotting stats, you need to use an external program (e.g. a bar plot in spreadsheet, or in matlab).
Often people report effects and p-values in a table but bar plots or box plots may be visually more appealing.

Pct. Change of global brain:
the global brain volume is reported in the header of the stats files in freesurfer and should be part of the table produced in your second command? Note that the total brain volume in freesurfer is not directly estimated but is the sum of some structures, minus some others (e.g. ventricles). Because of that it may not be one of the most reliable measures that FS reports. Probably looking at WM volume and total GM volume is better.

Best, Martin


On 10/03/2014 12:42 PM, Taylor North wrote:
  Hello Freesurfer community,
 
I am using the mri_glmfit model to analyze my group data at two time points.  First I ran the following commanded swapping pc1 with spc to get an image of the symmetrized percent change across my group.
 
-------------------------------------------------------------------------------------------------------------------------
long_mris_slopes --qdec long.testretest.qdec \
      --meas thickness \
      --hemi lh \
      --sd $SUBJECTS_DIR \
      --do-pc1 --do-label \
      --generic-time \
      --fwhm 15 \
      --qcache fsaverage \
      --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
      --isec-labels lh.testretest.fsaverage.cortex.label

mri_glmfit --osgm \
           --glmdir lh.testretest.thickness-pc1.fwhm15 \
           --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \
           --label lh.testretest.fsaverage.cortex.label \
           --surf fsaverage lh

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh
---------------------------------------------------------------------------------------------------------------------------------------
 
Next I ran the following command to get volume change results:
 
----------------------------------------------------------------------------------------------------------------------------------------
 
long_stats_slopes --qdec long.testretest.qdec \
      --stats aseg.stats \
      --meas volume \
      --sd $SUBJECTS_DIR \
      --do-pc1 \
      --generic-time \
      --stack-pc1 testretest.aseg-pc1.stack.txt

mri_glmfit --osgm \
           --glmdir testretest.aseg-pc1 \
           --table testretest.aseg-pc1.stack.txt

cat testretest.aseg-pc1/sig.table.dat
 
----------------------------------------------------------------------------------------------------------------------------------------------
 
The results from the volume command are all in a table which is useful however I was wondering if there also is anyway to get a visual picture of the percent volume changes like the first spc command provided?
 
Also is there any command that can give you the percent change in global brain volume?
 
 
Thanks for the help!
 
Cheers,
 
Taylor North 
  

-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu