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Are you writing spatially normalised fMRI at the same time?  If so, then the 
masked region may correspond to those parts of the fMRI where there is no 
data.  To fix it, you could write the spatially normalised anatomical image 
seperately from the spatially normalised fMRI.

As for the image that you attached, I have no idea what this is.

Best regards,
-John

On Wednesday 09 July 2008 18:27, Snehashis Roy wrote:
> Hi SPM-ers,
>
> I am having this trouble. I have a 256x124x256 volume, with resolution
> 0.9375x1.5x0.9375mm, origin at 128x62x128. As provided in the list,
>  I used the bounding box [[-119 120]' [-91.5 93]' [-119 120]']. I get a
> truncated image output where only top portion of the image has non-zero
> result and rest is thresholded. I believe it comes from a wrong masking
> somewhere. I checked the headers of both the original image and the mask
> image, they are exactly same.
>
> Please let me know what could be the problem.
>
> Thanks,
>
> ~snehashis