• View
• Edit
• History
• Print

PerformMRISegmentationWithBrainVisa

Open BrainVisa

Type brainvisa

Click on IRM T1

Open the folder "importation" Double click on "importation d'une IRM T1"

Input: open your file sequencename_flip3.ima Output: click on the red icon "Base de Données" and choose the output file, click on OK If necessary, choose:

Base de données: /neurospin/unicog/protocols/MEG/IRManat/BrainVisa Data type: raw T1 MRI File format: GIS Protocol: segmentation Sujet: entrer non du sujet (NIP) 2) Open the folder "Pipeline de Segmentation"

Double click on "Pipeline T1 2007"

Mri: open your original MRI file (no flip) Mri_corrected: open (if necessary) your corrected file and Save You now have to mark different anatomical landmarks

Anterior_Commissure, click on the Anatomist button In Anatomist, mark the anterior commissure by pressing the left mouse button and then, click in the brainvisa window to acquire the corresponding coordinates.

Do the same thing for the other anatomical points

Be carefull!!! In Anatomist: if you chose the Preference "Radiologic view" the right (left) hemisphere is on the left (right); The Preference "Neurologic view" displays the right hemisphere on the right.

The default setup is the Radiologic view. Thus, to keep the right on the right, acquire RPA coordinates from Anatomist in the LPA box in BrainVisa.

Select all operations excepted "Graphe des plis corticaux" and "Sulci recognition" (you don't need it). Execute the pipeline If one warning appears: select "Autoriser le flip des images IRM"

After these operations, you will have the following files:

		Nomsujet_head.mesh
		Nomsujet _Lhemi.mesh
		Nomsujet_Rhemi.mesh
		Nomsujet_Lwhite.mesh
		Nomsujet_Rwhite.mesh

as well as the corresponding files with minf extension