[caret-users] Monkey atlases

[John Harwell]

On Mar 4, 2008, at 3:34 PM, Alex Fornito wrote:

> Hi all,
> I have two questions:
>
> 1 - Exactly where can I download the Macaque datasets? Specifically,  
> I'm looking for the paint files for the various cytoarchtectonic  
> parcellation schemes. I've tried to download the Macaque atlas  
> specs, but all I get is the spec files, with no associated files. I  
> have been able to download some of relevant paint files as part of  
> some tutorial datasets, but I was wondering if there is one place  
> where I can find all the relevant files.
>

Are you trying to download the spec file through the SuMS database?   
If so, instead of selecting "Download" from the popup menu, select  
"Download Spec Listing as (zip)".

> 2 - Ultimately, I am looking to convert the macaque  
> cytoarchitectonic parcellations into volumes. Ideally, I would  
> convert say, the F99 scheme to one volume, with each region having a  
> different 'intensity' value in the volume. Is there a simple way of  
> doing this? The only way I could see was to use Region of interest  
> operations, select nodes within a certain paint column, and convert  
> them to a volume, but I had 2 problems with this: (1) I could only  
> figure out how to do it on a region-by-region basis, meaning that  
> trying to extract all regions would take a long time; and (2)  
> whenever I did try to create a volume, the file seemed to be  
> dimensionless; i.e., I could select a volume in the 'model' button,  
> but it appeared empty and I could not scroll through the slices. I  
> was wondering what the easiest way of achieving this goal is, and  
> where I am going wrong.
>

First, load fiducial coordinates, closed topology, the paint file, and  
the area color file.  Next, select Attributes Menu->Paint->Convert  
Paint Column to Paint Volume (http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/dialogs/Surface_To_Volume_Dialog.html 
).  In the surface selection, verify that the proper fiducial surface  
is selected.  The Inner Boundary and Outer Boundary are are set to  
-1.5 and +1.5 by default to approximate the thickness of a human  
cortex.  These should be adjusted to smaller values for monkey  
cortex.  You may also want to reduce the Intersection Step to a  
smaller value.  In the Volume Selection section, set the Space to  
MACAQUE-F99 which results in the new volume being in the F99 Space.   
In the Paint section, select the desired partitioning scheme from the  
Paint File.  Lastly, press the OK button and allow several minutes for  
the operation to complete.  This operation will create a new Paint  
Volume which must be saved in NIFTI (recommended) or AFNI volume file  
format using the File->Save Data File Dialog.  In the resulting paint  
volume, each voxel will be an integer value that indexes into a table  
of labels (partitioning scheme identifiers such as V1, V2, etc).  You  
can view the Paint Volume by making it an overlay on the Display  
Control's Overlay/Underlay - Volume page.  Just like the surface, you  
can click on a voxel and its identification information will be printed.


> Perhaps the surface-based cytoarchitectinic parcellations were  
> generated from volumetric data. If so, where could I download them?
>
> Any help is much appreciated.
> Thanks,
> Alex
>
>
>
>
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-----------------------------------
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