I'm measuring the total volume of grey and white matter in the frontal, parietal, occipital and temporal lobes in a bunch of subjects (T1W). But I am not sure that my method is the most appropriate...
1. BET the subject
2. FLIRT MNI152_T1_2mm_brain to subject_bet and save the transformation to affine.mat
3. FNIRT MNI152_T1_2mm (with skull) to subject (with skull) and save the warp
4. I have an atlas in MNI152 space with labels for the four lobe (left and right hemispheres), diencephalon, pons and cerebellum. I ApplyWarp the warp from step 3 to this atlas
5. FAST subject_bet
6. I wrote a command to count the number of grey and white matter voxels in each of the lobes (using the FASTed subject and the warped atlas).
In particular, I'm a bit uncomfortable transforming the atlas into the subject instead of transforming the subject into the atlas, but inverting the warp was taking too much time.
Thank you for your help!
cheers,
roberto
