Automated Web-Reports for a FreeSurfer Subjects Directory

[hebbianloop]

Surfer Web-Gems

Demo

Project Description

This software in development takes a FreeSurfer subjects directory, runs some summary routines, spits out meta-information to screen/tsv, compiles papaya web viewers for each subject, and generates a folder of html files running the papaya js to show individual subject brainmasks, edits, atlases, parcellations etc. etc. and across-subject summaries (SNR/p(edit voxel)/morphometrics).

This project was somewhat sloppily developed in bits and pieces over the period of a year and needs a bit of consolidation and help from individuals with software packaging experience (I'm a bit of a novice).

Skills required to participate

Experience with nipype
Structural imaging (freesurfer?)
Bash scripting?
Java scripting

Need someone to help compile surface viewers to embed in HTML hereto docs.

Integration

This package would help groups easily parse output and summary statistics of the FreeSurfer pipeline for large datasets, aiding neurologists, clinicians and scientists to easily parse and view data.

Some goals

Everything is was slapped/taped/glued together using bash as a wrapper for calls to various neuroimaging softwares and using HERETO documents to automatically generate HTML webpages. A bit of clean-up, integration with python, documentation and expansion of functionality are the immediate goals (roughly in that order).

• Rewrite FreeSurfer subject's directory summaries using nipype
• Consolidate all functions and calls into a singular repository (this bridges two right now)
• Output meta-analytic data to JSON rather tsv
• Complete cross-subject summaries
• Add 3D surface viewers for pial/white surfaces with thickness/morphometric overlay

Preparation material

🤷‍♂️🤷‍♂️🤷‍♂️🤷‍♂️

Link to your GitHub repo

Surfer-webgems
[Dependent on Surfer-gems](git clone https://github.com/seldamat/Surfer-gems.git)

Communication