If you transform the coords in the GUI, make sure you save the resulting coord file as a different filename (e.g., my_subject.R.fiducial.native.coord).
On 02/25/2010 10:43 AM, wolf zinke wrote: > Hi Donna, > > Thanks a lot for this comment. Now I can go and have a nice sleep... > > wolf > > > On 02/25/2010 04:16 PM, Donna Dierker wrote: > >> Hi Wolf, >> >> If it makes you feel better, you could apply the inverse transform to >> your surface coordinates (see Window: Transformation Matrix Editor or >> caret_command -surface-apply-transformation-matrix), so that you can map >> your Z-map directly to the "native" surface. >> >> I hope others speak up if they disagree with me, but reporting >> interpolated z-values should be pretty far down on your stack of things >> to worry about. >> >> It would be different if this were a label/ROI file you were mapping, >> but then you would use nearest neighbor (NN). Of course, that is >> another alternative -- using NN for your Z-map. But I'm guessing these >> are bigger fMRI sized voxels, so there are concerns there. >> >> I think you'll sleep better if you bring your surface to your volume. >> >> Donna >> >> On 02/25/2010 03:16 AM, wolf zinke wrote: >> >> >>> Hi, >>> >>> I am sorry for this naive an likely many time answered question, but a >>> first search did not bring up any clear statement to this issue. >>> >>> I use caret to view functional data on inflated monkey brains. The data >>> was analysed with FSL on data oriented according to a coordinate system >>> based on eye and ear bars, but the caret files use the >>> anterior,posterior commisure, hence I apply a transformation to my >>> thresholded functional data (z-values) including a trilinear >>> interpolation. This of course lead to subthreshold values surrounding >>> the patches, and reduced, more smooth values within patches. In the step >>> of mapping the volume data to the surface I again apply >>> interpolation/averaging of the z-values. >>> >>> I am wondering now, if this is an accepted procedure and that the >>> interpolation of statistical maps is in general not seen as a serious >>> problem. Though the statistics of the maps are reduced and smeared, I >>> doubt that this introduces a serious misplacement of the activation >>> foci. However, I don't fell well to present the range of z-values as >>> 'z-values' anymore, because of the interpolation. >>> >>> I am happy for any pointers regarding such issues. >>> >>> thanks, >>> wolf >>> >>> _______________________________________________ >>> 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
