Hi,
It depends on what the size of the image you have been given is.
Check it against the $FSLDIR/data/standard images or the "standard"
image in the FEAT directory. If they are different then you cannot
use it directly. You can resample it with the following command though:
flirt -in yourmask -ref standard -usesqform -applyxfm -out newmask
then you can use newmask image.
This assumes that the image you were given has the correct
coordinate transform embedded in it. You could check this in
FSLView to see if the mm coordinates reported there really are
MNI coordinates. If not, you'll need to get your ROI some other way.
All the best,
Mark
On 18 Nov 2011, at 14:26, David S Chester wrote:
> Hey Mark,
>
> I got the mask image from someone else at a different university. I contacted them and they told me the mask images were indeed in MNI standard space, but that they were also 1mm. Could this be the root of the problem if my functional/anatomical data is in 2mm?
>
> Cheers,
> Dave
>
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