Freesurfer Guide (Mac)

FreeSurfer is an open source software suite for extracting the cortex from an MRI, and more.

I’m using Brainstorm, but Brainstorm cannot extract the cortex from the MRI so I need to do this with FreeSurfer. There are also other utilities like BrainSuite that can do this as well.

Step 1

Download Freesurfer here.

Step 2

Register for a license key here.

Step 3

Follow the installation instructions. Create a license.txt file, copy the key into it and save in the freesurfer folder.

Sourcing FreeSurfer Mac from terminal:

$> export FREESURFER_HOME=/Applications/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh

Step 4

Navigate to your DICOM folder in terminal.

Run the recon-all command

recon-all -i file.dcm -subject NAME -all

Where file.dcm should be one of the DICOM files in your folder (e.g. 00000001.dcm or just 00000001). Freesurfer will automatically get the rest of the images in the series.

After the -subject argument NAME should be the name you want to call the study/subject. There will be a folder created with this name in the Applications/FreeSurfer/Subjects folder.

The process can take 10-20 hours, for me, it took ~10hrs on my 2011 core i5 Macbook Pro.

screen-shot-terminal-freesurfer

Once it is done you can proceed to import your Freesurfer anatomy into Brainstorm. See the tutorial here.

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