[caret-users] importing thresholded functional data

Donna Dierker donna at brainvis.wustl.edu
Thu Feb 25 09:16:13 CST 2010

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.


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
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