Head mask/MRI after importing

1

Hello Francois,

I sometimes have these weird artifact appearing after importing a freesurfer folder.

  1. head mask with extra "skin" layers / skull deformities ?
  2. CAT12 segmentation with bottom filled as if it was also skin.

However when I take a look at the MRI I see none of those and the quality is good.

Interesting is that when I import the same MRI but segmented with brainsuite I do not see these "artifacts".

For one of old post back in 17' , you mentionned to "right-click on the MRI > Compute head surface", but I don't see this option in brainstorm now, and is it a problem with the MRI or am I doing something wrong unpon importation from FS.

Thank you

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2

I sometimes have these weird artifact appearing after importing a freesurfer folder.

There is some artifact in your MRI scan: right-click on one of the slices in the MRI Viewer and move your mouse up, you will see that the intensity is much higher around the chin.
Unfortunately, I can't help you with this. You need to ask the FreeSurfer or CAT12 developers how to pre-process the MRI to get rid of this bias before processing it.
Or if it works with BrainSuite, then maybe use BrainSuite instead.
@CGaser @Anand_Joshi ?

you mentioned to "right-click on the MRI > Compute head surface", but I don't see this option in brainstorm now

It is named "Generate head surface" now.

3

Hello Francois,

Sorry, just catching up on the my previous posts in the forum.

Thank you for the advice (using another segmentation tool, and generate head surface) help alot.

Thanks