[caret-users] Monkey atlases

Tue Mar 4 17:42:13 CST 2008

There are several templates...

D99 and probabilistic ones are here:
http://sumsdb.wustl.edu/sums/directory.do?id=6653275

F99 and F6 locations will need to come from John, David, or Donna.

On Tue, Mar 4, 2008 at 5:21 PM, Alex Fornito <fornitoa at unimelb.edu.au>
wrote:

> btw - is there anywhere that I can download the volume of the macaque
> template?
>
> 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
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> caret-users mailing list
> >> caret-users at brainvis.wustl.edu
> >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> >
> > -----------------------------------
> > 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
> > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
> 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
>
>
>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>

-- 
Best Regards, Donald McLaren
=====================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
=====================
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