Dear FSL community
I have a single group of individuals with baseline and follow-up DTI scans (varying interscan intervals). I'm using fsl maths to calculate the difference between each individual's two scans (fslmaths subject1_rA -sub subject1_rB sub1_diff) and merging to create a 4D image, as suggested in the wiki page.
Which two files should I be using as the input though?
When I try to use individuals' baseline and follow-up FA files, a warning message comes up saying "Inconsistent orientations for individual images in pipeline! Will use voxel-based orientation which is probably incorrect". Presumably, this is because they haven't been normalised to the same template yet? So does that mean I should be using target files instead e.g. BL0005AS_FA_to_target.nii.gz -sub FP0005AS_FA_to_target.nii.gz sub1_diff?
Also, the FSL wiki also has a FEAT setup which seems quite a different approach to the above. Could anyone explain which one is appropriate when?
Thanks very much for your help!
Cheers, Ellen.
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