Perform MRI Segmentation With Brain Visa
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