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

Tue Aug 5 08:40:05 CDT 2008

... this time with capture attached.

On 08/05/2008 08:38 AM, Donna Dierker 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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