Hi Veena,
> 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?
Yes, make sure that they have the correct name...
> The struc
> directory has files
> other than the _struc_brain. What do I do to get those?
I am not sure which files you are referring to, so I don't think you would need them.
> 2) I realize that for the same patients, Freesurfer has
> produced much better
> brains. Can I use these extracted brains to run fslvbm??
I can't see any reason why you should not. Again, make sure they have the appropriate name.
Cheers,
Gwenaelle
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