gridgen

Preparation of the data

For this analysis, you will need a structural MRI and an angiogram.

1. Angiogram

Realign the angiogram to the structural MRI and rename it to angiogram.nii.gz.

Mask the angiogram with outskull, so that you don’t get veins in the skin.

If the angiogram has a resolution higher than 1mm isotropic, you can also resize to 1mm. This will speed up the calculation without impacting the results.

flirt -in angiogram.nii.gz -ref angiogram.nii.gz -applyisoxfm 1 -o angio_1mm
mv angio_1mm.nii.gz angiogram.nii.gz

2. Freesurfer

Run recon-all on the structural MRI.

After running Freesurfer, you will have the files:

3. Create a convex hull of the pial surface

3.1 Bash

mris_fill -c -r 1 lh.pial lh_filled.mgz
mri_convert lh_filled.mgz lh_filled.nii.gz
fslmaths lh_filled -kernel 3D -dilF lh_dilated

3.2 Matlab

addpath('/path/to/freesurfer/matlab/')
make_outer_surface(...
  'lh_dilated.nii.gz', ...
  15, ...
  'lh.outer', ...
  1)

3.3 Bash

mris_smooth -nw -n 60 lh.outer smooth.pial
mv lh.smooth.pial lh_smooth.pial

4. Summary of files

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