Dear Zeyu,
> I'm trying to perform VLSM on patients with cerebellar lesions.
> I'm using 3mm clinical scans that only includes the cerebellum and
> not the anterior commissure. I isolated the cerebellum by hand and
> now I'm trying to normalize the cerebellums to the same space for
> lesion analysis. I'm going to be using the SUIT cerebellum atlas by
> Diedrichsen and al. found here
> ( http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm ) as the
> template. I changed the origin to 72 48 44 (4th ventricle) on the
> atlas with MRIcro and matched the origin on the patient scans to the
> same location. I tried using the included spm toolbox that came with
> the template, but with no success (think it's because the toolbox
> assumes origin at the AC and normalizes the cerebellum coordinates
> with reference to the AC).
>
> I tried FLIRT, the results looked okay, and now I would like to try
> FNIRT.
> Does resetting the origin to somewhere else affect the FNIRT
> normalization process (I assumed as long as the origin matched
> everything should be fine)?
the origin should be of no consequence. If you have a good flirt
registration that you can pass in as starting guess for fnirt you
should be fine.
> What settings would be best for the configuration file when using
> the SUIT template? Have you guys ever worked with the template
> before, maybe you could send me a configuration file you used.
If I remember correctly Diedrichsen used fnirt and our "regular"
T1_2_MNI152_2mm.cnf file in his 2009 paper. So that would be my
starting point.
Good luck Jesper
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