[caret-users] How to export the template image of Macaque in "hdr/img" form

[Donna Dierker]

Sorry I didn't get to this yesterday; I was busy breaking a colleague's
computer.  As I explained off-list, there are several parcellation schemes
for the macaque, and it isn't obvious which is the best choice for you,
since we don't have a "AAL" scheme.  There is a Brodmann scheme with this
comment: "Brodmann (1905) cytoarchitectonic areas initially mapped onto
manually generated flat map by Van Essen & Maunsell (1980) then registered
to atlas map using surface-based registration constrained by sulcal/gyral
landmarks."  But other schemes, like LVE00, might better serve your
purpose.  I've attached an excerpt (label_columns.txt) from the F99
composite paint file that lists some candidates with their comments.

If you decide the LVE00 scheme works for you, then you're in luck, because
the September 2006 tutorial dataset includes a volume with that scheme
(see attached capture).  Browse the PDF file in the CARET_TUTORIAL_SEPT-06
directory (http://sumsdb.wustl.edu/sums/directory.do?id=6585200) to see
how to access it.

Otherwise, if you decide to stick with Brodmann, say, then here is how you
would project the surface paint parcellation to a volumetric ribbon:

1.  Launch caret5 and navigate to the downloaded and extracted
CARET_TUTORIAL_SEPT-06 directory, MACAQUE subdirectory.

2.  Open spec file Macaque.F99.BOTH-HEMS.STANDARD-SCENES.73730.spec; press
the Load Scenes button.

3.  Double-click the "Lobes + geo-blend on Flat (Macaque F99 BOTH)" scene
in the D/C menu (list of scenes).

4.  Select Paint Selection from the D/C Page Selection menu (top).

5.  Select the "Brodmann - Macaque.F99UA1.R" column.

6.  Select Attributes: Paint: Convert paint column to paint volume.

7.  Adjust the ribbon thicknesses, if desired; the default +/- 1.5mm works
well for humans, but is probably too thick for monkeys.  Someone who knows
the right thickness should chime in (e.g., DVE).

8.  The choice of target volume is worth considering, and it should match
the surface.  You probably don't have a preference now, but might in the
future.  For now, if you use
Macaque.F99UA1.RIGHT.FIDUCIAL.Std-MESH.73730.coord for your surface, then
choosing Macaque.F99UA1.LR.03-11+orig.BRIK as your volume (via Get
parameters using volume file) should work well.  Before clicking OK, make
sure the paint column is correct.

9.  Save the resulting Volume Paint file as AFNI or WUNIL ifh format.  I
think those are the only two formats that work for paint volumes.  Once
you write the volume, then you can open it in Caret as a Volume Anatomy or
Volume Functional, and then save it in another format like NIfTI or
Analyze, if desired.  But the label-number lookup won't be included.

Repeat this process for the left hemisphere, using
Macaque.F99UA1.LEFT.FIDUCIAL.Std-MESH.73730.coord (the same volume should
work for both).  Note that you'll have separate left and right volumes. 
You could combine them into a single volume, but there are no guarantees
that the label-number lookup will be the same across hemispheres.

The .ifh or .HEAD header of the resulting paint volume does contain the
lookup (LUT) information; I'm not certain that it matches the lookup near
the header of the surface paint file.

Donna
>
> How to export the template image (such as Brodamnn) of Macaque in
analyzed
> form (hdr/img) with the label of each ROI reserved?In another word, is
it
> possible to obtain a template image with every ROI labled for the
Macaque,
> which is similar to the AAL or Brodmann template images available from
MRICro for human?
> The version of caret is 5.5. Windows XP system. As a rookie, detail
steps
> of caret are highly appreciated.
>
>
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