Dear Benjamin,
I didn't realise you were trying to use single voxels in structural space. These are just too small to register in your functional image - as they have very low partial volume. For example, your structural space voxel is of size 1x1x1mm but your functional voxels are 4x4x4mm, meaning that one structural voxel only represents 1.5% of the volume of a functional voxel. Hence it is always below threshold after it has been transformed.
The solution is to make a bigger voxel in the structural space (to be much closer to the size of a functional voxel) or to lower the threshold applied to the transformed mask using the -i option.
Alternatively, use the coordinates option, as that is what it is designed for. It is all explained in the documentation.
All the best,
Mark
On 17 Mar 2013, at 16:39, Benjamin Philip <[log in to unmask]> wrote:
> Mark-
> You have a point that featquery does correctly identify that my mask is in highres space. However, *something* is going wrong with the mask's transformation and registration: my original mask has values in it (confirmed by fslstats -R) but in the featquery output directory, mask.nii.gz has zero range.
>
> Further testing indicates that this problem (empty featquery masks) occurs for masks in either highres or standard space, but not for masks in functional space. Those work just fine. Yet the FEAT registration results look just fine also.
>
> I have uploaded my feat directory (including featquery outputs for all tests), highres anatomicals, original masks, and a short explanatory text file: https://www.dropbox.com/sh/0lm04l8bflowfaq/ajg7KmnPjr
>
> (Relevantly or otherwise, doing the applywarp without a --postmat as you suggested also leads to an empty (range 0) mask.)
>
> Thanks,
>
> Benjamin Philip
> University of Missouri
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