Greetings!
I am running fsl-vbm on 10 patients and 10 controls. After running
fslvbm_1_bet -N I realized that the output for 5 of my patients is really
bad. Lot of non-brain portions are retained. I re-ran using fslvbm_1_bet -N
-R('more "robust" brain centre estimation'), but the results are not much
better.
I have two questions-
1) should I run BET seperately on each of these 5 patients and then copy the
brain.nii.gz files into the struc directory? The struc directory has files
other than the _struc_brain. What do I do to get those?
2) I realize that for the same patients, Freesurfer has produced much better
brains. Can I use these extracted brains to run fslvbm??
Thanks in advance!
Veena.
|