I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work!
Josh
-


On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
oops, I meant the aseg.stats, not the aseg.mgz

On Wed, 30 Nov 2011, Joshua Lee wrote:

Hi Bruce,

I'll see if I can phrase this right

In aseg.mgz each region has essentially been given a unique number (e.g. 17
for left hippocampus, for example). ROI taken from aseg.mgz volumes are
non-probabilistic, yes-no affairs already.  MRI_binarize just pulls this out
when we want to look at particular regions, say left hipp???

Josh




On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
     probably not, as the aseg.stats calculation uses partial volume
     estimates.

     cheers
     Bruce

On Wed, 30 Nov 2011, Joshua Lee wrote:

     Hey Doug, THanks. That looks simpler. I'll probably use
     that.

     Question: Will the total volume of a ROI taken from
     aseg.mgz correspond to
     the volume given in aseg.stats?

     Josh



     On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve
     <greve@nmr.mgh.harvard.edu>
     wrote:
          If you have matlab, you can load the aseg into
     matlab, like
          aseg = MRIread('aseg.mgz');
          vol = length(aseg.vol(:,:,n:256) == ID);
          where ID is the code number for the ROI you want  as
     found in
          $FREESURFER_HOME/FreeSurferColorLUT.txt
          doug

          Joshua Lee wrote:
     Hi All,

     I would like to determine the volumes of a segmented
     region
     below or above an arbitrary line in one of the planes. For
     example, what would be the remaining volume of a label
     when z >=
     nth slice, where I would have previously determined the
     appropriate value of n.



     Thanks,
     Josh
     ------------------------------------------------------------------------

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     Douglas N. Greve, Ph.D.
     MGH-NMR Center
     greve@nmr.mgh.harvard.edu
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