brain mask for preprocessing and NODDI fitting

[Andra Braban]

Dear NODDI experts, 

 

I am working on the pre-processing of DWI data to be used in the NODDI analysis and I would like to know what brain mask would be best to use during the Eddy distortion correction step using eddy_openmp in FSL, and subsequently when applying the NODDI model. Would it be fine to use a brain mask obtained from the T1 images (after running BET and manually cleaning the mask), transformed to DWI space using a 6DOF transformation? Or should BET be applied to B0 / HiFi_B0 from the topup output directly?

 

I would be very grateful for your advice.

 

Kind regards,

Andra 

[Hui Zhang]

Hello Andra,

I usually apply BET directly to the first b=0 volume.  By choosing the value for “-f” option with a bit of trial and error, I tend to be able to  get satisfactory results.

Gary

--
You received this message because you are subscribed to the Google Groups "NODDI" group.
To unsubscribe from this group and stop receiving emails from it, send an email to noddi+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/noddi/c2516a96-0a38-4b77-b549-d9e76d8f038an%40googlegroups.com.