A software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
FreeSurfer provides a full processing stream for structural MRI data, including:
- Skull stripping, B1 bias field correction, and gray-white matter segmentation
- Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
- Labeling of regions on the cortical surface, as well as subcortical brain structures
- Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
- Statistical analysis of group morphometry differences
Using FreeSurfer on RCC Resources#
To run FreeSurfer, you need to add it to your path and run the setup script:
For 6.0.0, run the following commands:
For Version 7.1.1, run the following commands:
You need to define the
SUBJECTS_DIR variable, as if you don't, you will get write permission errors due to FreeSurfer
defaulting to the location it is installed in, which is not writable. Change
YOURFSUID/path/to/output in the
SUBJECTS_DIR to your FSUID followed by the file path where you want the output to go.
Once the FreeSurfer setup is complete, you can use FreeSurfer as shown in the documentation.
Running FreeSurfer in Parallel#
The primary method of running FreeSurfer in parallel is to use the GNU Parallel library. Instructions on how to run commands in parallel can be found at this FreeSurfer Tutorial site. Below is a sample Slurm Script for the "recon-all" tool:
Then submit your script using the following command, replacing
YOURSCRIPT with the name of your script file:
You may need to modify find
. -name "*.nii" such that the find command starts at the top level directory where your
data is stored. You can also just use the
cd command to change to that directory, then run the
find command as it is
written in the above example. You may also need to modify the last command to work for different tools.