[caret-users] Monkey atlases
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.
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
> 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
> caret-users mailing list
> caret-users at brainvis.wustl.edu
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