Hello,
You can use the fslorient tool to modify your mask image sforms so that they can be read into matlab. Note that after the matlab processing you will need to restore the original sform before continuing to process with FSL.
Kind Regards
Matthew
> Dear FSL experts,
>
> I have been analyzing my data with FSL and with complementary matlab scripts.
> I am using native space and have functional files and mask files of specific ROIs.
> After applying XFM in FSL, some of my mask files cannot be read into matlab in the nifti toolbox because of non-orthogonal rotations.
> Is there any other way to read a mask file into matlab?
>
> Thank you very much for your help!
>
> Meytal
