[Mne_analysis] Anatomical ROI coordinates

[Matti Hamalainen]

Hi Chris,

On Jun 3, 2009, at 9:56 AM, Chris Andrews wrote:

> I am working on a project where we would like to incorporate  
> anatomical
> information into our results.  We essentially need to be able to  
> load the
> ROI's produced with mne_add_patch_info and the Deskian ROIs in
> the same coordinate system.
>
> We sourced MEG data to agnostically assigned ROIs (labels; using
> mne_add_patch_info producing *-l/rh.label) and would like to find a
> relatively easy and automated way to figure out to which anatomical
> regions these ROIs/labels correspond. We thought we could find some
> coordinates in the .label files that might correspond to the  
> anatomical
> Desikan ROIs automatically produced by freesurfer. The  
> agnostic .label files
> seem to have coordinates in them. However the anatomical Desikan  
> ROIs do
> not seem to have any coordinates in them, yet we are able to view  
> them in
> mne_analyze. Does anybody know where those coordinates come from
> so that I can programmatically attribute the agnostic regions to the
> anatomical Desikan regions they are located in? Has anybody any other
> ideas how to easily and automatically figure out to which anatomical
> region the .label files correspond? We have 162 labels per hemisphere
> and a number of subjects so looking them up through mne_analyze  
> would be
> quite time consuming.

You do not, actually, need coordinates to do what you describe. You  
can work entirely with vertex numbers. However, you need to do a  
little bit of Matlab coding to achieve the result. Here is how:

1. Convert the Desikan parcellation to labels using mne_annot2labels

2. The newest MNE version 2.6.1 contains mne_read_label_file which you  
can use to read label files.

3. Load all the Desikan parcellation labels.

4. Using the 'intersect' Matlab function determine which Desikan  
parcellation labels has the biggest number of vertices common to your  
agnostic label of interest.

I hope this helps.

- Matti




---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu






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