[caret-users] A question when mapping a functional volume to brain surface

[Donna Dierker]

Hi Dr. Wang,

Are you by any chance using a BOTH spec file to display your results?  
When sorting out problems like this, I find it is helpful to use 
hemisphere-specific spec files.  For example, the CARET_TUTORIAL_SEPT06 
has these three spec files:

PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec
PALS_B12.LEFT.STANDARD-SCENES.73730.spec
PALS_B12.RIGHT.STANDARD-SCENES.73730.spec

If you are using PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec, then 
using PALS_B12.LEFT.STANDARD-SCENES.73730.spec and 
PALS_B12.RIGHT.STANDARD-SCENES.73730.spec independently, to see if your 
problem persists.  I suspect it might be mapping okay, but you are 
displaying the left hem result on the right hem, or vice versa.  Getting 
only one hem in your Caret session will help us rule out such problems.

The only other explanation I can come up with is unlikely.  If your 
volumes were Analyze, rather than NIfTI, then it might be possible to 
open the .hdr for one hem and specify a flip, but then open it for the 
other hemisphere and not specify a flip.  But I thought SPM5 wrote 
NIfTI.  (You might be able to specify Analyze, though.)  Chances are, 
though, you didn't open your volume through the File: Open Data File: 
Volume Functional file dialog anyway, which is the only way you are 
prompted for a flip.  If you load through the mapping wizard, it simply 
doesn't flip.

Let's start with the single hem specs and see where that gets us.

Donna

On 05/26/2009 11:57 PM, liang wang wrote:
> Hi CARET experts,
>
> Following the guideline, I successfully used CARET (v5.6.1) to map a 
> functional volume (SPM5 results) to PALS_B12*.spec. However, we found 
> that the displayed results differed from that from MRIcron or SPM5 in 
> the same threshold. Moreover, the results from CARET seemly were 
> symmetric across two hemisphere. Actual results were far away from 
> this situation. I attempted to adjust the threshold in the section 
> "Page selection - Metric setting" to see whether the results from 
> different software could match well. Unfortunately, it did not work 
> well. If you share a solution, I would be appreciated.
>
> Thanks in advance,
>
> Liang
>
>
> -- 
> Liang Wang, PhD
> Postdoctoral Fellow
> Woodward Lab
> Department of Psychiatry
> University of British Columbia
> BC Mental Health & Addiction Services
> 938 West 28th Avenue
> Vancouver BC V5Z 4H4
> Telephone: 1-604-875-2000 (ext. 4735)
> Fax: 1-604-875-3871
> Email: wanglbit at gmail.com <mailto:wanglbit at gmail.com>
> ------------------------------------------------------------------------
>
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