https://github.com/dangom/recon-all-lite

A minimal reimplementation of FreeSurfer's recon-all script.
https://github.com/dangom/recon-all-lite

Last synced: about 2 months ago
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A minimal reimplementation of FreeSurfer's recon-all script.

• Host: GitHub
• URL: https://github.com/dangom/recon-all-lite
• Owner: dangom
• Created: 2021-05-07T02:06:18.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2021-05-07T02:07:35.000Z (over 3 years ago)
• Last Synced: 2023-10-05T20:31:38.285Z (over 1 year ago)
• Language: Python
• Size: 10.7 KB
• Stars: 3
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.org

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README

        
#+TITLE: Recon-all Lite

* What is this?

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 [[https://snakemake.readthedocs.io/en/stable/][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.

* Dependencies

=recon-all-lite= is built with Snakemake, and thus depends on:

- FreeSurfer 7.1.1, and

- snakemake

* Usage

Use it as you would use any Snakefile workflow.

#+begin_src sh

# 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}

#+end_src