So, John and fellow SPMers,
Since we are trying to use SPM5 to do volumetric analysis of WM, GM and CSF, specifically looking at age effects and possibly longitudinal analysis in dementia and TBI patients, we really need either a reliable measure of CSF or at least a good measure of intracranial cavity volume (without dura, skull, etc.). Is there a good way of doing this in SPM proper or extensions of SPM? How have people done these analyses?
Randy
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Randall R. Benson, M.D.
Assistant Professor of Neurology
Wayne State University School of Medicine
UHC-8D 4201 St. Antoine
Detroit, MI 48201
Tel: 313-993-2726
Fax: 313-745-4216
-----Original Message-----
From: SPM (Statistical Parametric Mapping) on behalf of John Ashburner
Sent: Fri 4/4/2008 9:17 AM
To: [log in to unmask]
Subject: Re: [SPM] Segmentation-Results display
> We are trying to do volumetric analysis from segmentation using SPM5. We
> would like to get accurate measurements of GM,WM and CSF volumes. We are
> running into some problems.
CSF volumes are not likely to be very accurate, as there are no tissue
probability maps for non-brain tissues. Maybe the skull-stripped version
would help here - but be careful not to strip out too much CSF.
>
> 1) We are finding that when we skull strip the MPRAGE, the segmentation
> algorithm never gives a solution. Has anybody else observed this?
Depending how the skull-stripping is done, it is possible that the orientation
information in the headers is being lost, or filled with junk.
> 2) When we apply a mask of the brain to the MPRAGE image in segmentation,
> which of the 3 options (data, probability map, mask) should be used?
Masking is just for cases where there are lesions in the brain, which you
don't want to influence the way that GM, WM etc in other parts of the brain
is segmented.
> 3) There is no result displayed on the graphics window after the
> segmentation program is done- Does anybody know why this is the case?
Because I was too lazy to write the code for displaying the results. It is
easy to check the results with the Check Reg routine, and this allows you to
display the images that you consider most useful.
> 4) There is no PS file written in the working directory after the
> segmentation program is done.- Does anybody know why this is the case?
Again, because I was too lazy.
Best regards,
-John
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