Hi Annelene,
The easiest way is possibly:
1. Create your ROI in the space of the atlas
2. Use FLIRT to resample the ROI into the space of the standard, e.g:
flirt -applyxfm -usesqform -in my_mask -ref
$FSLDIR/data/standard/MNI152_T1_2mm -out my_resampled_mask
Cheers,
Paul
On Wed, 24 Jul 2019 at 15:33, Annelene Dahl <[log in to unmask]> wrote:
>
> Hi!
> I'm trying to create an ROI from an atlas file which has the same resolution as the standard brain, but not the same (x,y,z) size. They both overlay perfectly in FSLeyes. I have tried selecting the region from the atlas in FSLeyes, and pasting it into a new mask file the same size as the standard brain (not the atlas image), but this doesn't work.
>
> I also cannot extract the mean timeseries from the ROI unless the mask size is the same size as the functional data (which is in the template space).
>
> Does anyone have any idea how to do this?
>
> Thanks!
>
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