36. Quick sheet about Freesurfer reconstructions

file structure

An environment variable $SUBJECTS_DIR should be set first. Within the subject folder, files are organized as the following:

---

SUBJECTS_DIR

• subject 0001
  • mri
    • transforms
    • orig
  • surf
  • label
  • bem
  • stats
  • scripts
  • tmp
  • trash
  • touch
• subject 0002
• subject 0003

---

file formats

Freesurfer reconstructions use different file formats for different purposes

• .mgz, .mgh: brain volume images (3D); typically within mri folder
• lh.xxxx, rh.xxxx: brain surface models and information; typically within surf folder

Some details for each folder

NOTE: useful page here.

NOTE: You can use freeview for visualizing brain volumes and surfaces as shown below.

• mri

  • orig.mgz: the MRI used for reconstructing everything
  • T1.mgz: the MRI after intensity normalization (and other correction)
  • brain.mgz: brain volume after skull stripping
  • wm.mgz: white matter volume
  • aseg.mgz: brain segmentation labels
  • orig.mgz: the input MRI volume for FreeSurfer reconstruction

• surf

  • ?h.pial: pial surface model
  • ?h.smoothwm: white-gray matter boundary surface model
  • ?h.inflated: inflated brain surface model
  • ?h.sphere: spherical brain surface model
  • ?h.curv: local cortex curvature
  • ?h.thickness: local cortex thickness

• label

  • ?h.aparc.annot: ROIs for cortical parcellation

• stats

  • brainvol.stats: brain volume information

• bem This folder is typically used in EEG/MEG source modeling to store Boundary Element Model data.

NOTE: All vertices are consistent across brain surface models. This means that vertex #1 in lh.pial, for example, is the same vertex #1 in lh.inflated. The difference is the vertex coordinates in different models. The (x,y,z) of vertex #1 in lh.pial is different from (x,y,z) of vertex #1 in lh.smoothwm. Surface triangulations are the same but their 3D coordinates are different across models.

Visualization in Matlab

1. Cortical thickness (in mm).

val=inverse_read_curv_new('lh.thickness'); hist(val,100); %show the histogram of left hemisphere cortical thickness

2. Show brain surface model

[vv, ff] = read_surf('lh.smoothwm'); %matlab routine in $FREESURFER_HOME/matlab/read_surf.m
figure; patch('vertices',vv,'faces',ff+1,'edgecolor','none','facecolor',[1 1 0].*0.7); lighting phong; camlight; axis vis3d equal;

3. Show brain surface model with cortical thickness

val=inverse_read_curv_new('lh.thickness');

[vv, ff] = read_surf('lh.smoothwm');

fvdata=repmat([1 1 1],[size(vv,1),1]);
    
c_idx=find(val(:)>=1.5);
overlay_cmap=autumn(80); %overlay colormap;
fvdata(c_idx,:)=inverse_get_color(overlay_cmap,val(c_idx),3,1.5); %get color for vertices with thickness > 1.5 mm; the color is saturated at 3 mm
    

figure; 

patch('vertices',vv,'faces',ff+1,'edgecolor','none','FaceVertexCData',fvdata,'CDataMapping','direct','facecolor','interp','edgecolor','none');   

lighting phong; camlight; axis vis3d equal;

4. Show brain volume

v=MRIread('brain.mgz');
fmri_mont(v.vol);