Hi again Hamied,
One minor clarification regarding the thickness. Since the macaque
cortex is only ~1.5 mm thick, you should modify the default settings
to a smaller value. Good results come from a choice of +/- 0.75 mm,
though you can fine tune that if you are doing detailed quantitative
studies that are sensitive to cortical thickness estimates.
Note that the macaque F99 atlas volume is 0.5 mm voxel size, but the
paint to volume operates on mm not voxels if the volume file header
has the appropriate metadata.
David VE
On Jan 7, 2008, at 11:28 AM, John Harwell wrote:
Hamied,
1) Load the Macaque surface and paint file into Caret.
2) Select Attributes Menu->Paint->Convert Paint Column To Paint
Volume.
3) In the dialog that appears, use Surface Selection to choose the
fiducial surface in the Surface Selection section of the dialog. In
the Volume Selection Dialog, press the Get Parameters Using a Volume
File and select the Macaque Anatomical volume which results in the
Volume Selection parameters matching the anatomical volume. In the
Paint section of the dialog, choose the parcellation that you would
like to see in a volume. Press the OK button to create a new paint
volume which may take several minutes.
4) Use the Display Control to view the new paint volume.
5) Use the File Menu->Save Data File dialog to save the new paint
volume. Use the NIFTI format (the AFNI and WUNIL formats can also
be used for paint volumes).
In the Surface Selection section, the Inner Boundary and Outer
Boundary determine the estimated thickness of the cortical surface.
These default to -1.5mm and 1.5mm which approximates the typical 3mm
thick human cortex.
Good Luck.
-----------------------------------
John Harwell
[EMAIL PROTECTED]
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave Box 8108
Saint Louis, MO 63110
On Jan 7, 2008, at 10:58 AM, Hamied Haroon wrote:
Dear Donna and David,
There are about 12 different cortical parcellation paint files
available in Caret for Macaque F99UA1 (right hemisphere). However,
only LVE00 is mapped onto the anatomical MRI volume
(Macaque.F99UA1.LR.03-11+orig.HEAD) as well as the surfaces. Is
there anyway, in Caret, to map one of the other cortical
parcellation paint files onto F99UA1’s anatomical MRI volume, in
the same way as was done for LVE00? I would be grateful if you
could please let me know.
I look forward to hearing from you.
Many thanks in anticipation.
Hamied
________________________________________________
Hamied Ahmad Haroon PhD AMInstP
Research Associate in MR Neuroimaging
Imaging Science and Biomedical Engineering Research Group
School of Medicine
Faculty of Medical and Human Sciences
The University of Manchester
Room G.603 Stopford Building, Oxford Road,
Manchester M13 9PT
England, United Kingdom
Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145
Email: [EMAIL PROTECTED]
Web: www.isbe.man.ac.uk/~hharoon
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