Skullstrip example

This example pipeline reconstructs the skullstripping-pipeline originally defined in the niworkflows Python package from the Poldrack-lab. This pipeline loads a T1-weighted structural scan, applies bias field correction (using ANTs) and intensity harmonization (using AFNI), skullstrips the image, and finally writes the results to disk.

Skullstripping workflow including bias field correction and intensity harmonization

Note that this pipeline includes Nipype-based nodes from three different major neuroimaging packages (ANTs, AFNI, and FSL).

Check out the Porcupine-generated Python-script, Porcupine-pipeline, and associated Dockerfile in our Github repository or download the files directly below.

Download .pork-file Download .py-file Download Dockerfile