gyrification index

Questions about BrainVisa usage and installation

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joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

gyrification index

Post by joost »

Hi,

i want to calculate a g-SI (global sulcal index) as described in (Cachia et al., Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations, NI, 2007).

four questions:
- in the paper it reads: "The hemispheric outer cortex area was defined as the area of a smooth envelope of the brain mask. The envelope was obtained with a morphologic closing of the brain mask; an isotropic closing of 5 mm was used to ensure the boundary smoothness."

1) does the "hemispheric outer cortex" refer to the file L/R_cortex*.ima (segmentation)?

2) when generated with "Ana Compute Cortical Fold Arg", does this L/R_cortex*.ima already contain the "morphological closing"? i think the answer to this question is "yes", from looking at the output of "VipHomotopicSnake".

3) which command could i use to calculate the surface area of the L/R_cortex*.ima segmentation?

- The paper: "The total sulcal area was calculated as the sum of the area of all the segmented cortical folds"

4) does this mean that, in order to calculate the total hemispheric sulcal area, one should simply sum the "surface areas" of all folds as stated in the L/R*.arg file in the graphe directory (from the "Ana Compute Cortical Fold Arg" procedure)?

thanks!
-joost
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Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
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Post by Jean-Francois Mangin »

I am sorry this stuff is not in the current release,
as far ass I can see, the question is yes for everything. I prefer Arnaud
to give you the detail. One of the command of the package is giving the surface of a mesh, but you have to mesh the hull first. I want to be sure how Arnaud did it.
joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: gyrification index

Post by joost »

Hi,

is there an update on my 4 questions? that is, could somebody confirm whether this is the _exact_ right way to do it?

thanks,
-joost
PeterK
Posts: 45
Joined: Fri Mar 05, 2004 3:18 pm

Re: gyrification index

Post by PeterK »

We have developed some tools to do it using basic BVisa functionality

http://ric.uthscsa.edu/personalpages/pe ... Index.html


Look at the posters to see the validation
http://ric.uthscsa.edu/personalpages/petr/genetics.html
joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: gyrification index

Post by joost »

Hi,

yes, thanks. using version 3.1 now, a bit more user-friendly for calculating gyrification.

PeterK: your toolbox seems designed for version 3.02, is that correct?

merci.
PeterK
Posts: 45
Joined: Fri Mar 05, 2004 3:18 pm

Re: gyrification index

Post by PeterK »

Yes, it won't take us much time to redo the package for the new version. We just downloaded it today. Email me if you don't see it in a couple of weeks.
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