Perhaps this is a clue that you should actually be aligning subjects on
the surface and doing your group stats there.
Peace,
Matt.
On 6/3/18, 9:56 AM, "FSL - FMRIB's Software Library on behalf of Alon
Baram" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Hi,
>
>I have an image in native space, which has values only in a grey matter
>mask , and NaNs in the rest of the image (It's actually the output of an
>RSA analysis I've run on the surface with using the Freesurfer
>reconstruction). I want to move this image to MNI space to do group
>stats. If I use applywarp, I get many more voxels with NaNs in the output
>image than in the original image. I assume that's because for every voxel
>which has a NaN in the original image somewhere in it's vicinity,
>applywarp will use that NaN to interpolate. So the only voxels that
>survive are voxels in the middle of the grey matter, which are "padded"
>with other grey matter voxels, so they have no NaNs when interpolating.
>
>This is an issue because I end up getting one image per subject in MNI
>space with thin and non-matching NaN patterns, and I can't do group stats
>because most voxels in MNI space have at least one subject (usually many
>more with a NaN.
>
>I can't replace the NaNs in native space with zeros, because that would
>bias the transformed images toward 0 in voxels that are close to NaN
>voxels (close to the edge of the grey matter). (My images are of "1 minus
>correlation" values, i.e values between 0 and 2, so pushing voxels
>towards 0 has a huge effect).
>
>Is there a way to ask applywarp to ignore voxels that are outside a mask
>when interpolating? or any ideas how to solve this problem?
>
>Thanks very much!
>
>Best wishes,
>Alon
>
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