This is a minimal reimplementation of FreeSurfers recon-all script. It doesn’t support all of the features of recon-all, but mimicks the entire single-subject stream. It’s implemented as a Snakefile
, which is like a Makefile but written in a python-like language.
The goal of the project was to educate myself on the inner workings of recon-all, and learn where each file is coming from and where it is created in the pipeline.
As a side effect, recon-all-lite helped me minimize FreeSurfer’s implicit dependency on subject ID and SUBJECTS_DIR in order to run commands. That’s because by specifying, explicitly, all required inputs and all generated/modified outputs at each step, and leveraging snakemake’s dependency tracking algorithm, it is possible to determine which commands have to be run to generate any given file from the recon-all stream.
Some other ideas I’ve been toying with, which may end up here:
- Supplying my own brainmask to FreeSurfer to aid pial surface segmentation as part of the stream.
- Substituting the bias field correction algorithm.
- Injecting my own GM segmentation.
- Fine tuning parameters for generating surfaces out of 7T high-res data.
recon-all-lite is built with Snakemake, and thus depends on:
- FreeSurfer 7.1.1, and
- snakemake
Use it as you would use any Snakefile workflow.
# Run this to run the stream up until generation of white and pial surfaces
snakemake --configfile subjID.yaml --cores all surf/{l,r}h.{white,pial}