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

Wed Aug 6 07:54:27 CDT 2008

Hi Amit,

Please see these recent caret-users posts on the same topic:

http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001468.html
http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001470.html

Donna

On 08/06/2008 02:06 AM, Amit Etkin wrote:
> Hi Donna,
>
> Thank you for the prompt reply and the link to the data. So far I'm 
> making good progress on my mapping of functional to surface, but have 
> a question in the process...is it possible to display the right and 
> left hemispheres side by side (positioned correctly) at the same time?
>
> thanks,
>
> Amit
>
> On Tue, Aug 5, 2008 at 6:38 AM, Donna Dierker 
> <donna at brainvis.wustl.edu <mailto:donna at brainvis.wustl.edu>> wrote:
>
>     Hi Amit,
>
>     See inline replies below.
>
>     Donna
>
>     On 08/05/2008 01:20 AM, Amit Etkin wrote:
>     > 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:
>     As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so
>     write
>     your spm_T's out in .nii form for feeding to Caret.
>     >
>     > 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?
>     When I select the SPM2 space and select
>     Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730, I
>     get a window like the attached capture.  Note that there is a
>     distinction between the surface used for mapping and the surface used
>     for display.  Using the default selections in the attached capture,
>     Caret will map not only to the average SPM2 left surface, but also to
>     each of the contributing PALS left hems in SPM2 space, and then
>     average
>     the resulting 12 individual maps.
>
>     Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be
>     displayed on the SPM2 average fiducial surface.  But we usually don't
>     display fMRI results on average fiducial surfaces.  We usually use the
>     inflated, sometimes very inflated (for opercular results) or flat
>     surfaces.  We do use average fiducial surfaces generated for
>     study-specific purposes (e.g., to illustrate morphometric
>     differences).
>     But it can be a little misleading to display results the PALS average
>     fiducial, because the audience might be tempted to make the implicit
>     assumption that your subjects' anatomical features exactly match PALS.
>     While on a broad level this will be true, on a micro level it
>     won't be.
>     >
>     > 2. When I open a spec file it asks for the space...should I pick
>     what
>     > it defaults to or change it to SPM5?
>     This reminds me:  Tim Coalson has generated SPM5 surfaces which we
>     need
>     to package and release.  The only loose end is the cerebellar surface.
>     I must coordinate with David (and possibly Joern Diedricksen) on that.
>     Yes, Jay Hegde, I did not forget you; SPM5 surfaces are on the way
>     VERY
>     SOON.
>
>     For now, select SPM2 (the closest space).
>     >
>     > 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?
>     Use SPM5 to write your spm_T's as .nii to resolve this problem.
>     >
>     > 4. Do I need to flip along the X axis or change the location of the
>     > origin of my functional images? If so, how?
>     If you write as .nii, Caret will flip as needed.
>     >
>     > 5. Where do I get flat maps, inflated surfaces and brodman area maps
>     > like there are in the tutorial?
>     Here is the Sept 2006 tutorial dataset:
>
>     http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030
>
>     Here is the Sept 2006 tutorial document:
>
>     http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379
>
>     Click on the diskette shaped icon to download them.
>
>     Don't be intimidated by the size of the tutorial; skip to Part 5,
>     section 5.1.
>     >
>     > 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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>
>
>
> -- 
> Amit Etkin, MD, PhD
> Department of Psychiatry
> Stanford University School of Medicine
> 401 Quarry Road
> Stanford, CA 94305
> office: 650-725-6705
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