Reza,

If you have a bunch of surfaces to import, the caret_command utility is useful. See this script:

http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
login pub
password download

You'll need to tweak it (e.g., output type SPHERICAL -- see caret_command -help), and you probably don't caret about the part that generates sulcal depth (which will slow it down a lot). I think it's possible to run the registration without importing the upstream surfaces (white, pial), but you might consider doing so anyway, so you can end up with resampled "midthickness" surfaces on the same standard mesh. Up to you.

Donna

On 02/16/2007 06:19 AM, David Vanessen wrote:
Reza,

On Feb 16, 2007, at 3:48 AM, Reza Rajimehr wrote:

We have done an fMRI experiment in macaques and humans. The anatomicals of
macaques and humans have been fully reconstructed in FreeSurfer. The
functionals have been also analyzed in FreeSurfer/FS-FAST. We have
successfully imported some reconstructed surfaces (e.g. inflated surface)
and functional .w files into Caret using freesurfer2caret.sh (more
specifically, we have imported one macaque cortex, and the spherical
average of 10 human cortices into Caret). Now we want to deform/register
the macaque cortex to the human cortex in Caret to see whether the
functional activity patterns are topographically aligned across species,
and therefore test possible homologies (something similar to "Orban, Van
Essen, Vanduffel - TICS 2004 - Fig. 4"). I had some questions regarding
this analysis, and I would really appreciate any comments or suggestions:

1) It is recommended to do this analysis in the spherical space. We have
spherical surfaces of macaques and humans in the FreeSurfer format. Is
there any way to import the spherical surfaces from FreeSurfer to Caret?

Yes. Use the File: Import File: Import Freesurfer (Ascii or binary, as appropriate).

Similarly, is there any way to import the flattened patches from
FreeSurfer to Caret?

Yes. Do the same import operation, but after previously importing a complete surface.

2) For the macaque-human registration, should I deform my monkey's
cortex/hemisphere to the macaque F99 atlas, and my human's
cortex/hemisphere to the human PALS atlas, and then deform F99 to PALS?
Or, I can directly deform the monkey's cortex to the human's cortex
without using the atlases?

You have multiple options. 1) Register your macaque to your human, independent of VE-lab atlases, and using your own landmarks. Technically feasible, but I don't recommend this, because it inhibits comparisons across studies and across registration landmark choices.

2) Register your data to our F99 and PALS atlases, i) Then take advantage of our existing monkey-human registrations (see below). You can use existing 'deformation map' files to map data from monkey to human without re-doing the registration process.

ii) Start with our existing monkey-human landmarks (again, see below), then add or subtract landmarks in order to formulate your own hypotheses about homologies between species.

3) It would be great if you also refer me to the most up-to-date
documentation/tutorial describing the macaque-human deformation analysis.

http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 <http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06>
contains the tutorial document and datasets.

Part 4 of Caret_Tutorial_Oct06.pdf contains the latest story on monkey-human comparisons.

You can download the entire tutorial dataset ( CARET_TUTORIAL_SEPT06.zip ) OR just the relevant monkey-human comparisons: COMPARE_PALS_MacaqueF99.73730.spec (Single File Action: download spec listing)
AND/OR
Human_Macaque_COMPARISONS.RIGHT.STANDARD-SCENES.73730.spec


RegF99toPALS_Core-20-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_CORE-20-LDMK.73730.spec.deform_map
and
RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map

are the two deformation map files to focus on.

Let us know if there are other issues/problems.

David


Thank you,
Reza - Tootell/Vanduffel Lab

********************************
Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>

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