[caret-users] Monkey atlases

David Van Essen vanessen at brainvis.wustl.edu
Tue Mar 4 19:36:36 CST 2008


Alex,

You can go to
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6660535&archive_name=Macaque.F99.RIGHT.DEMO.73730.spec
and launch WebCaret (by clicking on the brain icon).

The pulldown 'Scenes' menu lists a set of 20 scenes that can be  
selected for viewing.   Scene 9 shows in Window 3 the macaque MRI  
volume with the Lewis & VE areas as a 'paint volume' created in the  
way that John's email described.  You can download this dataset using  
the download icon, and also create additional paint volumes as needed  
for other partiitioning schemes.

David

On Mar 4, 2008, at 5:42 PM, MCLAREN, Donald wrote:

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