I have been trying to do an atrophy correction procedure on my SPECT/MR
data, and wrote previously about how to do this. This is the procedure that
was recommended and that I have been following
* Coregister SPECT and MR.
* Segment the MR to obtain GM and WM in native space.
* Smooth the GM and WM by the PSF
* Warp the SPECT and the smoothed GM and WM according to the *_seg_sn.mat file
generated from the segmentation - making use of the preserve total option
(which applies a Jacobian transform, or "modulation"). Apply the usual
additional smoothing of the warped data (8-12mm??).
* Subtract the smoothed, modulated, warped, smoothed white matter (scaled by
some value) from the smoothed, modulated, warped SPECT, and divide this by
the smoothed, modulated, warped, smoothed grey matter.
* Mask out regions where the smoothed, modulated, warped, smoothed grey matter
has a value of less than about 0.05 - or use some form of explicit mask for
the SPM analysis.
I have hit a stumbling block when it comes to normalising my GM and WM and
coregistered SPECT image as I can not find a way to introduce the
*_seg_sn.mat file into the normalisation process. None of the options for
adding files seem to take mat file format. Could you please help me with
where I might add the segmentation mat file into the normalisation
procedure. Is it the template?
Could I instead just normalise the SPECT and segmented GM/WM images to the
I also thought that I would actually binarise the GM and WM images before
smoothing them to the PSF, so that I wouldn't be decreasing any of the SPECT
voxel values when i divide by the MR grey matter. Would I be introducing any
problems in binarising the segmented images?
Thanks very much