[caret-users] Mapping Paint areas from Surface to MRI

[John Harwell]

Hamied,

1) Load the Macaque surface and paint file into Caret.
2) Select Attributes Menu->Paint->Convert Paint Column To Paint Volume.
3) In the dialog that appears, use Surface Selection to choose the  
fiducial surface in the Surface Selection section of the dialog.  In  
the Volume Selection Dialog, press the Get Parameters Using a Volume  
File and select the Macaque Anatomical volume which results in the  
Volume Selection parameters matching the anatomical volume.  In the  
Paint section of the dialog, choose the parcellation that you would  
like to see in a volume.  Press the OK button to create a new paint  
volume which may take several minutes.
4) Use the Display Control to view the new paint volume.
5) Use the File Menu->Save Data File dialog to save the new paint  
volume.  Use the NIFTI  format (the AFNI and WUNIL formats can also be  
used for paint volumes).

In the Surface Selection section, the Inner Boundary and Outer  
Boundary determine the estimated thickness of the cortical surface.   
These default to -1.5mm and 1.5mm which approximates the typical 3mm  
thick human cortex.

Good Luck.

-----------------------------------
John Harwell
john at brainmap.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110



On Jan 7, 2008, at 10:58 AM, Hamied Haroon wrote:

> Dear Donna and David,
>
> There are about 12 different cortical parcellation paint files  
> available in Caret for Macaque F99UA1 (right hemisphere). However,  
> only LVE00 is mapped onto the anatomical MRI volume  
> (Macaque.F99UA1.LR.03-11+orig.HEAD) as well as the surfaces. Is  
> there anyway, in Caret, to map one of the other cortical  
> parcellation paint files onto F99UA1’s anatomical MRI volume, in the  
> same way as was done for LVE00? I would be grateful if you could  
> please let me know.
>
> I look forward to hearing from you.
>
> Many thanks in anticipation.
>
> Hamied
>
> ________________________________________________
>
>  Hamied Ahmad Haroon   PhD  AMInstP
>  Research Associate in MR Neuroimaging
>  Imaging Science and Biomedical Engineering Research Group
>  School of Medicine
>  Faculty of Medical and Human Sciences
>  The University of Manchester
>  Room G.603 Stopford Building, Oxford Road,
>  Manchester   M13 9PT
>  England, United Kingdom
>  Tel: +44 (0)161 275 6871   Fax: +44 (0)161 275 5145
>  Email: hamied.haroon at manchester.ac.uk
>  Web: www.isbe.man.ac.uk/~hharoon
> ________________________________________________
>
>
>
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