Dear FSL experts,
I've been having some probrems with getting my mask from standard space (registered with MNI brain template) to a native space of some images in my sample. I'm using I_std_inv.mat matrix file (one of sienax outputs) to get my mask into native space-it works perfectly fine for 51/60 images. Oddly all 9 images that fail are sagital images(although it works fine for 11 other sagitals).
I find it quite bizzarre that the transformation doesn't work properly, even though the segmentation works perfectly fine. Is there something wrong with the transformation matrix or has it something to do with the orientation of my images?
Lukasz
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