Get vertex coordinate in MNI space

Discussions
1

Hi all

I would like to parse my group analysis results in order to get information over significant activation.
once obtained the “significant” vertex how can I get its coordinate in, for example, MNI space ?

I got the coordinates of the SurfaceFile (e.g. tess_cortex.mat), but then ?

thanks in advance
Alberto

2

I forgot to add…get the coordinates by scripts, not using the user-interface
Alberto

3

Hi Alberto,

To convert from SCS to MRI:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems

To convert from MRI to MNI:
mniLoc = cs_mri2mni(sMri, mriLoc);

Cheers,
Francois

4

many thanks!

5

Dear francois

I’m actually having a problem with the call to :

mniLoc = cs_mri2mni(sMri, mriLoc);

in my script, in order to have sMri, I call

sSubject = bst_get(‘Subject’, ‘@default_subject’);
mri_file = sSubject.Anatomy(sSubject.iAnatomy).FileName
sMri = load (fullfile(brainstorm_anat_path, mri_file));

but…I get this variable

sMri.FileName = ‘/@default_subject/subjectimage_colin_1mm.mat’

which in turn, at line 108 of cs_mri2mni.m (sSubject = bst_get(‘MriFile’, MRI.FileName))
gives me an empty sSubject and thus the script fails at line 110.

I patched it by re-assigning sMri.fileName

sSubject = bst_get(‘Subject’, ‘@default_subject’);
mri_file = sSubject.Anatomy(sSubject.iAnatomy).FileName
sMri = load (fullfile(brainstorm_anat_path, mri_file));
sMri.FileName=mri_file;

and it works, but it’s not nice…
Did I messed up my db in some way?

thanks in advance
Alberto

6

Hi Alberto,

This FileName field you were getting from the MRI file was something remaining from a previous version. I removed it for the future versions.
I recommend you load the MRI using the following call, this is assigning correctly this FileName:

sSubject = bst_get(‘Subject’, 0);
mri_file = sSubject.Anatomy(sSubject.iAnatomy).FileName;
sMri = bst_memory(‘LoadMri’, mri_file);

Francois

7

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