Hi,
Yes, I would recommend that you binarise your mask.
You can do this with:
fslmaths mymask -thr 0.5 -bin binmask
where the output will now contain only zeros and ones.
You can also alter the threshold value if you didn't
want to keep the smaller values from the original mask.
All the best,
Mark
On 21 Nov 2011, at 17:21, David S Chester wrote:
> Hi Mark,
>
> I performed the FLIRT command that you suggested and lo and behold my ROI mask in now wonderfully oriented to MNI space and I no longer get an error when I'm running it in FEAT! Thanks so much!
>
> I had one last question though. When I look at it in FSLView, the intensity of the mask ranges from 1-70 from voxel to voxel. Do I need to remake the mask so that the intensity is always 1? Someone told me this had to be done for pre-threshold masking.
>
> Cheers,
> Dave
>
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