[caret-users] Monkey atlases

Alex Fornito fornitoa at unimelb.edu.au
Tue Mar 4 17:21:53 CST 2008

btw - is there anywhere that I can download the volume of the macaque  

On 4 Mar 2008, at 22:03, John Harwell wrote:

> 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
> _______________________________________________
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Alex Fornito
CJ Martin Post-Doctorial Fellow
Brain Mapping Unit
Department of Psychiatry
The University of Cambridge
Addenbrooke's Hospital
Hills Road, Cambridge
CB2 2QQ, United Kingdom

Tel:		+44 (0) 1223 336 582
Fax:  	+44 (0) 1223 336 581
Email:	af397 at cam.ac.uk

Australian details:
Melbourne Neuropsychiatry Centre
Deaprtment of Psychiatry
The University of Melbourne
National Neuroscience Facility
Levels 2 & 3, 161 Barry St
Carlton South, Victoria
3053, Australia

Tel:		+61 3 8344 1861
Fax:		+61 3 9348 0469
Email:	fornitoa at unimelb.edu.au

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