how to correct the head mesh

vsmuser · Post by **vsmuser** » Sat Jul 08, 2006 12:07 am

I am trying to extract the head mesh but there are two artifacts: one at the top of the head and one at the forehead. Lowering the threshold to 1370 gets rid of the large artifact at the top of the head but not the one at the forehead. The problem seems to be in the head mask, it leaks until the edge of the MRI. what else can i do to address this problem?

I tried editing the head mask manually by pressing the "pencil" icon of the BrainVisa interface but when I press "run" again, my changes are overwritten. How could i go about this?

thanks!

Manik · Post by **Manik** » Mon Jul 10, 2006 12:49 pm

Hi,

after correcting the mask, you must launch "Anatomy --> T1 pipeline 2004 --> validation --> Validation_3 Brain Mask from T1 MRI" in Brainvisa, choose your brain mask, and choose validation "lock", then run the process.
Now the brainmask is locked, so it won't be overwritten.

Post by **riviere** » Mon Jul 10, 2006 1:05 pm

Hi,
I'm not sure there is actually a validation stop for the head mask, I guess only the brain mask has been taken into account.
If you edit the head mask manually, then you have to finish the mesh manually, using the AimsMeshBrain commandline (outside of brainvisa). The head extraction process is a very light algorithm which was not meant to make a clean and robust head segmentation, but just have a rough mesh which allows to globally visualize where the head is. There are obviously many improvements to be done before it is considered reliable.
Denis

vsmuser · Post by **vsmuser** » Mon Jul 10, 2006 7:48 pm

There is an option in the head mesh dialogue to input a "remove mask" . In the documentation it says i can use it to "manually remove sharp edges induced by artifacts". How do i create this mask?

Post by **riviere** » Tue Jul 11, 2006 9:28 am

Hi,
if keep_head_mask is False, the head mask is just not written by the process. If it is True, the head_mask file will be written by the head mesh process. Then you can edit it manually. But then you will have to run the mesh creation command manyally (using the AimsMeshBrain command).
Denis

Jean-Francois Mangin · Tue Jul 11, 2006 9:51 pm

I vaguely remember there is also an option in the commandline to input
some binary mask that will be removed before the mesh (one of my famous collegues had horns...). You can do this mask the way you want, for instance with the ROI toolbox of Anatomist.