Importing Free Surfer thickness surface file

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François Leroy
Posts: 30
Joined: Wed Feb 22, 2006 5:22 pm

Importing Free Surfer thickness surface file

Post by François Leroy »

Hi,

This is more a comment than a question.

We used Free Surfer to compute cortical thickness across the brain. After running Free Surfer, data were imported in Brainvisa (in order to compute sulci) using the "Import from Free Surfer to T1 Pipeline" tool.

Then we tried to import the thickness surface file (with a gifti format). Unfortunately, the file is not properly registered with the Brainvisa T1. In fact the surface file is flipped.

Here is a very simple Talairach transformation file that registers the surface file. The following 4 lines need to be saved as a transformation file (with a .trm file extension) and then applied onto the surface file using the AimsMeshTransform command tool:
128 128 128
-1 0 0
0 -1 0
0 0 -1

Please note that the translation component of the transformation, ie [128 128 128], is given by the dimension size of the Free Surfer T1 weighted image (that has been imported into Brainvisa). In our case, the T1 dimension size was [256 256 256]. If your T1 image size were [a b c], the translation component would be [a/2 b/2 c/2].

I think this might help future users.
Francois
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Olivier Coulon
Posts: 176
Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
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Re: Importing Free Surfer thickness surface file

Post by Olivier Coulon »

Hi François,

this is a problem due to the GIFTI format and the referentials conventions (direct and undirect) in BV and FS. We have been meaning to fix it for a while but never found the time to.
Hopefully we will quite soon.

Olivier.
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
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