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]>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 > > > _______________________________________________ > caret-users mailing list > [email protected]http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- 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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