FreeSurfer surface-based work flow (Forrest version)

The Wiki of FreeSurfer is not well organized. Links are like Go-To statement. So instead of crawl over their links the next time, I would write done my own notes.

First, I have a NIFTI format data under my current folder and it needs to converted into MGZ format.

1$ ls
s108921-0002-00000-000001-01.hdr
s108921-0002-00000-000001-01.img
$ mri_convert s108921-0002-00000-000001-01.img 290.mgz

After that, create a folder 290 under $SUBJECTS_DIR.

$ mkdir ~/bin/freesurfer/subjects/290
$ mkdir -p ~/bin/freesurfer/subjects/290/mri/orig
$ cp 290.mgz ~/bin/freesurfer/subjects/290/mri/orig/

Then do the reconstruction
recon-all -all -s 290

Finally, check the surface
~$ tkmedit 290 brainmask.mgz -aux T1.mgz -surfs

(if you want to see the segmentation result, add this option, -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt )

and check the geometric features (left hemisphere)
$ tksurfer 290 lh inflated

I played with some epileptic patients (structural/anatomical) MRI data. And come up with a new topic I can do later.

References:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData

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