Thanks for the help everyone.
Wolf: I was wondering why you chose to do a nonlinear transform
(FNIRT) as opposed to the linear (FLIRT) transform.
Is non linear better when registering to an atlas?
Thank you all again,
Matt Hutchison
On Wed, May 12, 2010 at 1:01 PM, wolf zinke <[email protected]
<mailto:[email protected]>> wrote:
Hi Matthew,
On 05/12/2010 09:51 AM, R. Matthew Hutchison wrote:
Hi group,
I am starting with Caret and have gone through most of the
tutorials using the data sets provided. The images are fantastic.
The part I seem to be missing is actually getting *my* activation
maps so that I can view them on the inflated surfaces.
If you use the menu 'Attributes', you'll find at the bottom 'Map
Volumes(s) to Surface'. I guess that is what you want. Took me a
while to find it as well ;-) .
I was wondering if anyone has a guide, steps, or hints in
converting the output files from FSL FEAT (registered to a
standard atlas using FSL FLIRT) to files viewable with Caret.
It seems this is not included in the tutorials.
T map macaque data of my individual monkeys to the caret F99
atlas, I used FSL's FNIRT for a nonlinear transformation. Doing
this once in a way, that I was somehow satisfied with the result
allows me to apply the transformation on the statistical maps, if
they are in the individual monkey space. However, You might want
to use the F99 atlas already as standard template in the Feat
analysis (if it yields convincing results).
I attached a small script that transforms a set of nii.gz-Nifti
files found within a directory into a new space according to a
Flirt transformation matrix file (linear) or a 3D volume with
warp-coefficients (Fnirt, nonlinear). Maybe this gives you an
idea. I cannot guarantee that it is bugfree, but at least It did
work for me.
A search of the archive does not turn up any recent information
on the issue that I could find.
I am actually using macaque data but I figure the steps should be
the same as with the human but using the F99 atlas.
Perhaps I am just missing something obvious?
I understand that my data must be registered to the atlas space
that I wish to use in Caret.
But which FSL file should be used and what is the next step so
that I can view them?
If it is registered to the atlas then there should be no need to
segment the volumes again right?
You can use the zstat* images in the stats subdirecory of your
copes as statistical map that you transform to the standars F99
space. In this case you can utilize the F99 segmentation, without
segmenting the individual brains. However, in my opinion you are
loosing the specificity of the localization, which in my view is
one of the huge advantages of primate fMRI. So I do both, mapping
data on individual brains, but also map all individuals on the
standard atlas for comparision.
Thank you for any help (and patience for a novice),
I hope this gives you some pointers. Good luck anyway,
wolf
R.Matt Hutchison
--
R. Matthew Hutchison, PhD. Candidate
Centre for Functional and Metabolic Mapping
Robarts Research Institute
Cuddy Wing - 9.4T Suite
P.O. Box 5015, 100 Perth Drive
London, Ontario, Canada N6A 5K8
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<mailto:[email protected]>
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_______________________________________________
caret-users mailing list
[email protected] <mailto:[email protected]>
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--
R. Matthew Hutchison, PhD. Candidate
Centre for Functional and Metabolic Mapping
Robarts Research Institute
Cuddy Wing - 9.4T Suite
P.O. Box 5015, 100 Perth Drive
London, Ontario, Canada N6A 5K8
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
