Dear Jeff,
Have you tried masking with MRICro? I know a couple of
people in the same situation as you who did it using
SPM99 but i'm sure you can also implement it with SPM2
or SPM5. I think it's worth having a look at the
following tutorial to see how it works.
http://www.mrc-cbu.cam.ac.uk/Imaging/Common/epimasking.shtml
Hope this is what you meant you wanted to do...
Best wishes,
Elisabeth
Dr Elisabeth Rounis
MB PhD student
Sobell Department of Motor
Neuroscience and Movement Disorders
Institute of Neurology
University College London
--- Jeff Browndyke <[log in to unmask]> wrote:
> Listmates,
>
> I'm in the process of deciding how to best implement
> a non-atlas based
> approach to analyzing our fMRI data, and I would
> like to learn from the
> experience of others as to which materials and
> methods would be best for
> our needs. Since the patient population for which
> we have fMRI data is
> fraught with the presence of brain atrophy (some
> quite significant), it
> doesn't seem appropriate to warp to a common SPM
> template. Rather, I
> would like to draw anatomically defined masks for
> particular regions of
> interest and examine the activity characteristics
> within these regions
> (e.g., ratio of activated voxels to total voxels,
> mean activation of
> voxels in ROI, etc.). The ROIs would also provide
> us the valuable data
> of accounting for volumetric differences in these
> regions among the
> subjects, which can then be used to correct for
> activity/atrophy
> interactions.
>
> What tracing software for the creation of anatomical
> masks best works
> with SPM2 or SPM5? And, does anyone know of a
> primer, good methods
> paper, or workshop for how to implement this
> anatomical ROI/non-atlas
> approach in SPM2 or SPM5?
>
> My previous SPM experience has been confined to
> normal anatomy, so what
> we're hoping to do is a bit foreign right now. I
> want to do the right
> thing with this data and warping to the SPM template
> doesn't seem to be
> it. I know manual tracing will be a major pain, but
> I don't see any
> other way to work around the atrophy/function issue.
>
> Regards,
> Jeff Browndyke
>
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