I've been using fsl_anat to perform subcortical segmentation of T1 datasets. It usually produces several outputs among which 'T1_subcort_seg' (something like that), from which I can then derive the left and right volumes for different subcortical structures.
Now, when using defaced MRIs data, it doesn't give me this output anymore (it does produce a 'first' folder with a T1_all_fast_firstseg file, like the same one I'd get from running run_first_all).
Any idea on how to fix this or why this happens? (if useful, I am using MRI_deface to produce defaced .nii.gz files).
I would appreciate any help!
on a different note, anyone used MIST and knows whether, although in beta, it produced better results than fsl_anat on T1 images?
Thanks so much in advance people!