[caret-users] help mapping an SPM5 activation volume to a surface
David Van Essen
vanessen at brainvis.wustl.edu
Wed Aug 6 08:46:51 CDT 2008
Amit,
The answer to your question does depend a lot on whether you need the
left and right hemisphere surfaces truly side-by-side in the same
Caret window. If that is the case, then the links Donna pointed to
are the preferred way to go.
However, for many purposes, it is advantageous to view the left and
right hemispheres in separate Caret windows (sized identically, and
sometimes with the left and right hemisphere views yoked together).
To do this, it is easiest to start with an existing dataset that has
the relevant files loaded and display features conveniently set up.
More specifically, go to: http://sumsdb.wustl.edu/sums/humanpalsmore.do
In the PALS_B12.BOTH-HEMS.STANDARD-SCENES
row, select 'View Online (WebCaret) if you want a quick look at what's
in the dataset, and choose 'Go to Data Directory' if you want to
download it.
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595788&archive_name=PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec
is an archive that has standard scenes for both hemispheres.
Importantly, this setup allows data that differ for the left and right
hemisphere to be assigned separately to each surface. This capability
is powerful and flexible, but you do have to be careful that what you
see displayed is in fact what you want.
If you find an alternate set of surface configurations and data
assignments works better for you as a starting point, be sure to save
it as a scene so that you can use it as your own customized starting
point in the future.
David VE
On Aug 6, 2008, at 7:54 AM, Donna Dierker wrote:
> 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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>>>
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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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