Lost gray matter during segmentation

Wei Wang bmewang at YAHOO.COM
Thu Sep 18 05:48:35 CEST 2008

Hi everyone,

I'm trying to work with my own MRI data, and after I did the segmentation 
with volumesegment.m , when I examine the gray matter with sourceplot, it 
seems that fraction of the gray matter was not marked as gray matter.  They 
were left out for some reason.  For example, part of the visual cortex are not 
included in my gray matter.  Since the segmentation is done using SPM2, I 
read the SPM manual a little bit, and, in the manual, it says, 
"5.2.5 Clean up any partitions
This uses a crude routine for extracting the brain from segmentedimages. It 
begins by taking the white matter, and eroding it acouple of times to get rid of 
any odd voxels. The algorithm continues on to do conditional dilations for 
several iterations,where the condition is based upon gray or white matter 
being present. This identified region is then used to clean up the grey and 
white matter partitions, and has a slight in uences on the CSF partition.
If you find pieces of brain being chopped out in your data, then you may wish 
to disable or tone down the cleanup procedure."

So, I went into the volumesegment.m code, and set:
defaults.segment.write.cleanup   = 0; 

When I run volumesegment again, it seems to improve the results a little bit, 
but still, I'm loosing some gray matters.

I'm wondering if you have any suggestions?  Thank you very much for the help!

Wei Wang
Department of Physical Medicine and Rehabilitation
University of Pittsburgh

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