Exporting an entire sulci to matlab

[Betina Vase]

From other threads I understand that picking up a mesh with an entire labeled sulci from the .arg file, one need to add some coding. I presume (or hope) that I’m not the first one that aims at picking up an entire sulci, so I thought that someone might give a bit of help on:

1) Where in the program to add the code
2) What code to add (I’m unfortunately not familiar with Python)

Alternatively where do I start?

My ultimate goal is to get a mesh of central sulcus into Matlab.

Thanks a lot!

[riviere]

Hello,

You don't need to be a real python programmer to get a mesh of an entire sulcus, but there are a few manual manips.
It is possible to get the sulci (or just one sulcus) as a label volume: in BrainVisa, you can use the "create sulcus label volume" process, in morphologist/sulci/recognition (you need to be in "expert" user level to see it). It allows to output a volume containing the voxels of the sulci, with one value for each sulcus, and you can specify to keep only one sulcus.
Then you can remesh the entire sulcus, using commandlines: AimsMeshBrain preferably, or AimsMesh if the sulcus is in several parts.
But using python programming, it is possible to get and save back the meshes already existing in each node of the sulci graph making the selected sulcus. For this you can look at: http://brainvisa.info/doc/pyaims/sphinx ... -and-tests

Denis

[Betina Vase]

Hi again. Thank you for the quick reply! I have now extracted my sulci. How do I run the AimMeshBrain? Do i need python indstalled?

[riviere]

No, it is a command in the bin/ directory of the Bv package. You can run it from a shell. Use --help option to see the parameters.
Denis

[Betina Vase]

Thank you .
Does a point correspondence exist between the extracted sulci? And if so how is it established?

[Jean-Francois Mangin]

No, you can not get point correspondence. This is a very complex issue because some sulci are interrupted in some subjects.

[Olivier Coulon]

I discover this post a little late...
For the special case of the central sulcus you can use the Cortical Surface-> Referentials -> Sulcus Parameterization process. The central sulcus has ionly one component for most subject so it's easier to deal with.
The process provides a parameterization of the sulcus mesh. that can be used to establish point-to-point correspondence. You can use Cortical Surface-> Referentials -> inter-subject tools -> Remesh to Atlas for this.

A couple of warnings, though:
- these are level 2 processes so we do not provide much support for them. They should be provided in a more stable and documented state in a further release (next one, probably).
- the inter-subject correspondence provided by the parameterization has its limitation. I don't know what you are using it for, and it is still a topic of research...
You can refer to the folllowing papers if you want to know more about all this:

Cykowski MD, Coulon O, Kochunov PV, Amunts K, Lancaster JL, Laird AR, Glahn DC, Fox PT, The central sulcus: an observer-independent characterization of sulcal landmarks and depth asymmetry, Cerebral Cortex, 18(9):1999-2009, 2008.

Coulon O, Pizzagalli F, Operto G, Auzias G, Delon-Martin C, Dojat M, Two new stable anatomical landmarks on the central sulcus: definition, automatic detection, and their relationship with primary motor functions of the hand, in IEEE EMBC 2011, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.7795-7798, Boston 2011.

I hope this helps,

Olivier