How to put my anatomy in MNI?

Bugs
1

I load my MRI and anatomy template then my surface.
How can I put my 3D surface in MNI space?

Thanks
Luca

2

Hi Luca,

First, I would recommend you use the menu “Import anatomy” instead of importing separately the different files:
http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawViewer#Import_the_anatomy

The MNI coordinates are the MRI coordinates for a volume that was transformed to the MNI stereotaxic space. Brainstorm doesn’t do this.
The correct procedure for reviewing your source maps with MNI coordinates is to estimate the sources on the original MRI of the subject, then project them to a template anatomy (Colin27 or ICBM152).
http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects
http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer

Cheers,
Francois

3

FYI, there is now the possibility to compute MNI coordinates for individual subjects:
http://neuroimage.usc.edu/brainstorm/News#MNI_coordinates

4

Dear Francois,
It is great new! I’m currently using brainsuite for process MRI volume, but normalizing procedure is available just for the volume processed with freesurfer. Do I understand correctly?
In this case I need to switch from brainsuite to freesurfer.

5

For now, it only works for isotropic volumes (voxel size = [1,1,1]), but it should work the same way no matter what program you used for the segmentation (FreeSurfer or BrainSuite).
FreeSurfer always rewrites the T1 volume in a 256x256x256 volume with voxels of 1x1x1mm, so this MNI normalization is always available in Brainstorm.
BrainSuite doesn’t do it, so it depends on your MRI dimensions.

Have you tried to click on this menu “Compute MNI coordinates” but got an error message?

Francois

6

Yes, but just simply doesn’t work without error message.

7

Are your running today’s version of Brainstorm?
Is it the same if you open the MRI viewer, then click on “Click here to compute the MNI transformation” ?

8

I’m running April 2015 version. If click on Click here to compute the MNI transformatio…error message tell me that this function is available just for freesurfer

9

Could you update Brainstorm and try again?
(menu Help > Update Brainstorm)

10

screen error.png1344×756 33.9 KB

that is the message error that I get!
Thanks
Luca

11

I used now last version 7 May 2015, but I get same error. Probably as you told me before problem is in MRI parameters extracted by brainsuite

12

Yes, only the MRI with a voxel size 1x1x1mm are supported right now…
I’ll work in the next few months on a generic function to resample MRI volumes in Brainstorm.