[caret-users] map a functional volume (SPM2 results) to PALS_B12.RIGHT.STANDARD-SCENES.73730.spec

[John Harwell]

Midoli,

I mistakenly mapped your volume to a 711-2C space surface.  In  
addition, I used the PSYCH palette without interpolation.  If I map  
your volume to the SPM2 space and display the results using the FIDL  
palette with interpolation, I get the same result as you.

John

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On Jul 7, 2009, at 11:48 PM, midoli wrote:

> Hi, John:
>
> Thanks for your help. I will ask senior students if they are able to  
> write NIFTI Volumes (.nii).
>
> For .hdr files, I have followed your instructions.
> After mapping .hdr to Surface, It looks better than before (http://midodo.net/neuro/caret2/capture.tiff 
> ) but it doesn't look as perfect as what you did yesterday (the  
> attached file: pastedGraphic.tiff).
> The right spotlight (22, 54, 4) seems to be not as bright as  
> "pastedGraphic.tiff" does.
>
> I took the screenshots step-by-step:
> http://midodo.net/neuro/caret2/
>
> Did I do something wrong or set improper parameters?
>
> Thank you very much.
>
> .Midoli
>
>
> On Wed, Jul 8, 2009 at 12:56 AM, John Harwell  
> <john at brainvis.wustl.edu> wrote:
> Midoli,
>
> It appears that your volume is in radiological orientation (it has  
> the left on the right).  Unfortunately, there is nothing in the  
> Analyze file format that provides orientation information and the  
> Map Volume to Surface assumes the left is on the left.
>
> What you can do is use File Menu->Open Data File to read your volume  
> file and you will be asked if the volume is in radiological  
> orientation so answer yes.  Next, use Map Volume to Surface and when  
> selecting your volume, press the Add Loaded Volumes button and  
> select the volume you loaded using Open Data File.  Continue the  
> process as you have previously and your data should be mapped  
> correctly.
>
> It appears that the volume was written by SPM.  If your version of  
> SPM is able to write NIFTI Volumes (.nii) instead of Analyze Volume  
> (.hdr) use NIFTI.  The NIFTI format contains all of the needed  
> orientation information.
>
>
>
>
>
> -----------------------------------
> John Harwell
> john at brainvis.wustl.edu
>
> Department of Anatomy and Neurobiology
> Washington University School of Medicine
> 660 S. Euclid Ave   Box 8108
> Saint Louis, MO 63110
>
>
>
>
> On Jul 7, 2009, at 10:03 AM, midoli wrote:
>
> Hi CARET experts,
>
> I used CARET (v5.6.1) to map a functional volume (SPM2 results) to  
> PALS_B12.RIGHT.STANDARD-SCENES.73730.spec.
> We expected there will be three spotlights.
> -- 1.(42, -60, 34), 2.(26, 26, 62), 3.(22, 54, 4)
> -- P< 0.01, k >10
> However, we found that the displayed results differed from what we  
> expected.
>
> I took the screenshots step-by-step and upload the .hdr and .img  
> files to this directory:
> http://midodo.net/neuro/caret/
>
> Any help is much appreciated.
> Thanks,
>
> Midoli
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