Render brain and check brain coordinates
Run the codes below will bring up the inflated brain surface reconstructed by FreeSurfer. As you click on the brain surface, another window with orthogonal brain slices will show. Press "w" will bring up a window showing the coordinates of the clicked points.
You can click either points at the inflated brain surface or at the orthogonal brain slices. The selected location in both surface and slice brain window and the associated coordinates will update accordingly.
We report 3 coordinates: the coordinate at the inflated brain surface (surface coordinate), the coordinate at the brain slices (voxel coordinate), and the coordinate of a standard brain atlas (MNI coordinate).
For every click, there are two markers in the figure. The blue circle marker shows the nearest gray matter (as defined by the brain surface, typically the gray-white matter boundary). The pink cross marker shows the actual selected location.
Note 1: Setenv was meant to guide the right folder location for all FreeSurfer reconstruction. This should be changed accordingly.
Note 2: you need to provide the brain volume in the orig.mgz. This is how FreeSurfer maps between volume and surfaces of the brain.
close all; clear all;
setenv('SUBJECTS_DIR','/My/path/to/subjects/');
mri=MRIread('/My/path/to/subjects/s012/mri/orig.mgz');
etc_render_fsbrain('surf','inflated','hemi','lh','subject','s012','vol',mri);
view(-90,30);
You can load an annotation file as following. Here we use the Broadmann's Area of the left hemisphere as an example.
file_annot='/My/path/to/subjects/s012/label/lh.BA.annot';
Then you call this:
etc_render_fsbrain('surf','inflated','hemi','lh','subject','s012','vol',mri,'file_annot',file_annot)
After the inflated brain shows up, press 'L' to bring up the list of labels defined by the selected annotation file. You can click on the list and the selected label will be displayed with color.
