What script are you referring to?
If it is the aff2rigid script, that is part of FSL, then it is designed to work with the MNI152 templates and will create outputs in this space. If you want it in a different space then you'll need to apply the output transform separately, with a separate reference image. Like all of our registration tools, it relies on the FOV being sufficient for the transformation. So the number of voxels isn't so important, but the FOV in mm is.
Have a look at the documentation and course material on registration for more information about resampling into different resolutions and FOV. If that doesn't answer your question then let me know more details, particularly of the script you are referring to.
All the best,
On 14 Apr 2013, at 22:21, Monica Giraldo <[log in to unmask]> wrote:
> Hi Mark, thank you for sharing that script. I just used it and worked fine but there's something I don't understand. The image I want to aligne to ac-pc is in proton density space and has dimensions 512x512x96. When I want to apply the transformation that your script generated it works fine if I concatenate empty slides and use an image of 512x512x512 but it doesnt work if I use the original image and Number of voxels 512x512x96. You know why this can be? As well if I want to register this image to any other space selecting the option Base on Voxel Dimensions in the Output Size in the APPLYXFM GUI, it only works when I use the dimensions 512x512x512.
> Thank you,