exclude MRI slices before segmentation

[elabyt]

Hello,
I would like exclude some MRI slices before the segmentation step. Do you know how can I do this (if it's possible) in Brainvisa or Anatomist?
Thanks !
Etienne

[Jean-Francois Mangin]

At the very beginning of the bias correction process, there is a parameter used to exclude
the N last slices of your image. It is especially useful when dealing with sagittal or coronal
acquisition covering the head till the neck. The lowest part of the head indeed adds a lot
of unusual intensities disturbing histogram analysis.

If you want to do something more complicated, you can use the AimsSubVolume command
to extract a block of slices before importing the volume into BrainVISA

[elabyt]

Hi Jean-François,
Could you give me more details ? Which parameter can be used to exclude the last N slices in the Biais correction process ?
I saw in the module "correction brain mask from T1 MRI" two parameters entitled "first slice" and "last slice". When I use this, the brain mask obtained seems to be OK but I don't know how to use this afterwards for the segmentation...
Thanks for your help !
Etienne

[Jean-Francois Mangin]

If you click on the T1 bias correction in the pipeline, the last parameter
is delete_last_n_slices. This will be propagated to the rest of the pipeline.
I think the way you did it is OK, except bias correction
and histogram analysis did not enjoy getting rid of the bad slices.