Pipeline for generating the cortical surface from Hyperfine pediatric brain MRI
You will need to download each of these four tools individually to run this pipeline. Installation instructions for each tool can be found at the provided links.
- FSL
- ANTS
- FreeSurfer (dev version ubuntu22-7-dev_amd64)
- Infant FreeSurfer (version linux-centos7_x86_64-infant-dev-4a14499)
For members of NeuroPoly lab; bireli has all of these versions installed. Just type fs infant in the terminal in order to change the version of FreeSurfer to Infant FreeSurfer.
This script expects your input image to be named T2w.nii.gz and be inside the data folder. If you have Hyperfine images of 3 orientations and wish to proceed with an isotropic reconstruction, 3 images must be inside the data folder and respectively be named AXI.nii.gz, SAG.nii.gz and COR.nii.gz.
Once your image is inside the data folder, navigate to the cortical-surface64mT repository in your terminal and type bash scripts/cortical_surface.sh to launch the pipeline.
After running the cortical_surface.sh script, you can go inside your FreeSurfer subject folder and open surf/rh.pial and surf/lh.pial in Freeview to visualize the pial surface of the brain.