Dear Claire,

> I would like to create a grey-matter mask (normalized) for my functional
> volumes and was wondering which preprocessing order is the ideal (or
> commonly used).
> For example, my functionals were realigned and then slice-timed -->
> coreg:estimate&reslice (resliced since I need to make the dimension of T1
> and that of functional same): used the mean functional as the reference and
> T1 as the image to write --> segmented the T1 --> normalize:write for the c1
> (grey matter) and functionals, separately using the ~sn.mat file created
> from segmentation....

In general that seems reasonable; t doesn't really matter at what
point you write out the normalized gray matter image. A few comments
though:

1) You will probably want to create a thresholded, binary gray matter
mask; otherwise, even voxels with very small values in the segmented
image will be included in your analysis (since they are > 0), which is
probably not what you want. You can do this in ImCalc. For example,
to only include voxels with a probability of 0.1, you could use the
statement: i1>0.1.

2) Because you are probably interested in the gray matter probability
value for thresholding, when you normalize the gray matter
segmentation I would use the "preserve concentration" (i.e.
unmodulated) option.

3) If you are smoothing your functional data, you may also want to
smooth the gray matter segmentation before creating the binary mask,
otherwise you may underestimate the spatial extent of the expected
gray matter signal.

4) I wouldn't reslice your structural image before segmentation; it
may not matter much in practice, but in theory I suspect you would get
more accurate segmentation if you segment the original image (since
there is more data available).

5) Although limiting your analyses to gray matter voxels is a
reasonable away to constrain your search space, keep in mind that
because it changes the overall smoothness of the search volume it may
affect cluster-extent corrections (so it may not buy you as much as
you think).

Hope this helps!

Best regards,
Jonathan

--
Dr. Jonathan Peelle
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/