[caret-users] help mapping an SPM5 activation volume to a surface

[Amit Etkin]

Hi all,

I'm trying to map my activation map (spm_T's written out as .img and .hdr
pairs) from SPM5 onto a surface in Caret, and getting more confused the more
I do. I've gone through the tutorial, can map activation files and can even
get my activation file mapped, but have a number of questions about how I
should go about doing that below:

1. Which spec file should I use? If I want to do the MFM approach, then it
seems I need to select the
Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730
file, for example, but it doesn't seem to have surface with the 12 subjects
averaged. If I want to get the averaged surface, in which case I can only do
AFM registration, I can chose
Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then can't do MFM.
I'd like to be able to do MFM but display it on the averaged surface...is
that possible? If so, how?

2. When I open a spec file it asks for the space...should I pick what it
defaults to or change it to SPM5?

3. When I map functional volumes to surfaces, I'm only given the option of
selecting between .hdr not .img files, and then get the warning: "You have
selected a ".hdr" file. If this ".hdr" file does not contain an SPM
originator, it is unlikely that it will get mapped to the surface
correctly". What does this error mean, and how do I know if the hdr contains
an SPM originator?

4. Do I need to flip along the X axis or change the location of the origin
of my functional images? If so, how?

5. Where do I get flat maps, inflated surfaces and brodman area maps like
there are in the tutorial?

that's all the questions I have for now, and would GREATLY appreciate all
the help I can get.

many thanks,
Amit


-- 
Amit Etkin, MD, PhD
Department of Psychiatry
Stanford University School of Medicine
401 Quarry Road
Stanford, CA 94305
office: 650-723-2516
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