fpizzaga/sulci repository overview

The Sulci protocol combines Freesurfer (https://surfer.nmr.mgh.harvard.edu/⁠) and BrainVISA (https://brainvisa.info/web/⁠) to robuslty segment and label 123 sulci across the whole brain. While BrainVISA is well designed to combine these tools using the GUI, having a practical command-line script to run thousand of subjects in parallel, on a computational cluster, is particularly suitable. This is why this protocol has been created.

For each sulcus, 4 sulcal shape descriptors are measured: length, mean depth, width and surface area. These features are then used for statistical analyses, such as correlations with behavioral scores, age, and genetic associations.

This protocol has been built in the context of the ENIGMA-SULCI working group (http://enigma.ini.usc.edu/protocols/imaging-protocols/⁠) and it has been already used for several publications, among others:

• Pizzagalli, F., Auzias, G., Yang, Q. et al. The reliability and heritability of cortical folds and their genetic correlations across hemispheres. Commun Biol 3, 510 (2020). https://doi.org/10.1038/s42003-020-01163-1⁠
• K.L. Grasby, N. Jahanshad, J.N. Painter, L. Colodro-Conde, J. Bralten, D.P. Hibar, N. Shatokhina The genetic architecture of the human cerebral cortex, Science, 367 (6484) (2020) https://www.science.org/doi/10.1126/science.aay6690⁠

Acknowledgments:

• ENIGMA: http://enigma.ini.usc.edu⁠
• BrainVISA: https://brainvisa.info/web/⁠
• Freesurfer: https://surfer.nmr.mgh.harvard.edu/⁠

Running the protocol is straighfarward using a Docker contantainer:

docker run -it --rm \
  -v $FSDIR:/fs_data \
  -v $OUTPUT:/output \
  fpizzaga/sulci subjectID

• FSDIR has to be the path, in the host machine, to the folder containing the subjects pre-processed with Freesurfer
• OUTPUT is the path to the folder, in the host machine, where the output of the Sulci-protocol will be saved
• subjectID is the ID of a subject to be analyzed, as listed in FSDIR