[caret-users] importing thresholded functional data

wolf zinke zinke at brain.uni-bremen.de
Thu Feb 25 10:43:38 CST 2010

Hi Donna,

Thanks a lot for this comment. Now I can go and have a nice sleep...


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
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