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ImportMRIForBrainstorm

Go to neurospin/unicog/protocols/MEG/myproject/my subject/IRManat

Open NMR server

Tape NmrServer

	Select your exam number (ask this one to the nurse)
	Add
	Choose "GIS conversion"
	Run

You now have to flip your images to put them into the proper orientation For this, use these successive command lines:

	VipFlip –i sequencename.ima –o sequencename_flip1.ima –m yz
	VipFlip –i sequencename_flip1.ima –o sequencename_flip2.ima –m xy
	VipFlip –i sequencename_flip2.ima –o sequencename_flip3.ima –m xx

(note: be careful when you copy paste directly from this page, some character might give errors. Example:

 VipFlip –i flip1.ima –o flip2.ima –m xy   --> give an error message
 VipFlip -i flip1.ima -o flip2.ima -m xy   --> work as intended)

The slices in 'sequencename_flip3.ima' are in the proper orientation: right is on the right. In Anatomist: if you choose the Preference "Radiologic view" the right (left) hemisphere is on the left (right); The Preference "Neurologic view" displays the right hemisphere on the right.

Open BrainVisa

Tape brainvisa

Click on IRM T1

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

If necessary, choose:

2) Open the folder "Pipeline de Segmentation"

Double click on "Pipeline T1 2007"

You now have to mark different anatomical landmarks

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

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

Import your MRI in Brainstorm

From matlab, tape brainstorm

Brainstorm opens and you have a graphic interface.

Create your new protocol (if you have not yet one)in your folder

    /neurospin/unicog/protocols/MEG/yourstudy/

Create your new subject (right click on your protocol name on the left part of the window)

Go to the MRI sheet (the left one)

Import your MRI (right click on your subject name)

Choose your MRI file

Double click on the MRI object to open the MRI viewer

Import the surfaces (right click on your subject name)

Import simultaneously the three files

Reduce the number of vertices for your head surface by using the menu "Less Vertices" (right click). Choose 8000. A new object nomsujet_head_8000V is created.

Merge both hemispheres models to obtain the cortex.

Reduce the number of vertices for your cortexsurface by using the menu "Less Vertices" (right click). Choose 15000. A new object cortex_15000V is created.

Delete files Lhemi, Rhemi and cortex and only keep Head_8000V and cortex_15000V.

Test the surface alignment of your surfaces with the MRI. For this, use the menu "Align/Check Alignment with MRI" (right click on the cortex_15000V object)