dear FSL experts,
I’m trying to create a tract specific mask based on my mean_FA_skeleton_mask, using fslview.
however, the orientation of the mask created is flipped.
I tried to use fslswapdim and fslorient to flip the L-R orientation,
but when i do so i get a different qto_xyz:1 than the one in the header of the mean_FA_skeleton,
and so the when trying to multiply the mask with the mean skeleton I receive the following message:
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
i would really appreciate your help. Why was the mask that I created not in the same orientation as the images it is based on?
many thanks,
Shir
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