Hi,
I'm new to FSL.
Could you please help me on these 3 questions?
1) I'd like to register a participant skull-stripped brain to an MNI brain,
which reference image do I use in FLIRT (and why) e.g.
152MNI_T1_2mm_brain.nii.gz ; avg152MNIT1_brain.nii.gz?
2)when I use std2imgcoord in order to convert MNI coordinates in the
coordinates of the registered braindo I have to put the same reference image
I used in FLIRT?
e.g. if in FLIRT I used as reference image avg152MNIT1_brain.nii.gz
do I have to do:
-std2imgcoord -img skullstrippedimage_brain.nii.gz -std
/usr/local/fsl/data/standard/avg152T1_brain.nii.gz -xfm
native2MNI_FLIRTtransformationfile.mat ?
3)what does -xfm stands for and in which units are the coordinates that come
out from std2imgcoord ?
I thank you in advance for your help!
ila
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