Dear Fernanda,

> I've been using FNIRT for registration to the MNI template. I'm
> using the following commands:
>
> FLIRT
> /Applications/FSL/fsl/bin/flirt -in /Users/fernandapalhano/Data/Aya/
> LET/Antes/FABIO/betted_Fabio_LET_ST001_RLPAIS_brain.nii.gz -ref /
> Applications/FSL/fsl/data/standard/MNI152_T1_2mm_brain -out /Users/
> fernandapalhano/Data/Aya/LET/Antes/FABIO/
> flirtedFabio_LET_ST001_RLPAIS_brain.nii.gz -omat /Users/
> fernandapalhano/Data/Aya/LET/Antes/FABIO/
> flirtedFabio_LET_ST001_RLPAIS_brain.mat -bins 256 -cost corratio -
> searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp
> trilinear
>
> FNIRT
> fnirt --in=Fabio_LET_ST001_RLPAIS --
> aff=flirtedFabio_LET_ST001_RLPAIS_brain.mat --
> config=T1_2_MNI152_2mm.cnf --cout=coef_Fabio_LET_ST001_to_MNI152 --
> iout=fnirted_Fabio_LET_ST001 --jout=jac_Fabio_LET_ST001_to_MNI152 --
> jacrange=0.1,10
>
> The problem is that some cortex voxels appears to be skull voxels
> after registration, or even they are completely out of the MNI
> template. I'm using the default parametres for both FLIRT and FNIRT.
> Am I doing anything wrong? How can I obtain better results?
> Besides, I'm wondering if there is any kind of measure to verify how
> good is my registration.

there is nothing obviously wrong with your commands (apart from maybe
a penchant for very long filenames) so it is not easy to say what has
gone wrong. Possible explanations are

1. The betting of betted_Fabio_LET_ST001_RLPAIS_brain.nii.gz went
wrong and too much of the brain was eaten away. That would lead flirt
to expand the remaining brain to fill the whole brain of the template.
This would mean that a "too large brain" was passed in to fnirt,
something I know from experience it has difficulties coping with.

This you can check by looking at the betted image, and also by looking
at flirtedFabio_LET_ST001_RLPAIS_brain.nii.gz to make sure that the
affine registration worked well.

2. You are attempting to register a non-T1 weighted image (e.g. a T2
weighted one) to our T1 template. This is something one can do with
e.g. flirt, but which is not possible/recommended with fnirt.

If neither of these are the case I think I would need more information
about how the registration has gone wrong from you.

Jesper