dbkeator
commented
5 years ago Additional skills: A good appreciation of Japanese sake may also help for late night discussion.
Open dbkeator opened 5 years ago
dbkeator
commented
5 years ago Additional skills: A good appreciation of Japanese sake may also help for late night discussion.
hebbianloop
commented
5 years ago This would be great to incorporate into https://github.com/seldamat/Surfer-webgems! The parent CLI spits out a lot of meta-data grabbed from the FreeSurfer Subjects Directory and it would be ideal to convert this to JSON. Would love to collaborate.. i also would not mind sake as an accompaniment to hacking!
satra
Name of your awesome project
Awesome Script to Export Freesurfer-based Parcellation/Segmentation Stats and Provenance as JSON-LD and NIDM
Project Description
This project ultimately aims to facilitate both query and analysis of parcellation/segmentation based regional statistics across popular softwares such as Freesurfer, FSL, and ANTS. Currently each software produces its own output format and brain region labels are specific to the atlas used in generating the regional statistics. This makes life difficult when trying to search for "nucleaus accumbens" volume, for example, across the different software products. Further, knowing which version of the software tool used and what atlas and version of the atlas in a structured representation facilitating query is lacking. To this end we propose augmenting the various segmentation tools with scripts that will: (1) map atlas-specific anatomical nomeclature to anatomical concepts hosted in terminology resources (e.g. InterLex); (2) capture better structured provenance about the input image(s) and the atlases used for the segmentation; (3) export the segmentation results and the provenance as either JSON-LD, NIDM which can then link the derived data to broader records of the original project metadata, or as an additional component of a BIDS derivative.
We aim to tackle this problem in steps. For this hackathon project we'll be focusing on conversion from Freesurfer's mri_segstats program output along with some additional parsing/conversion of Freesurfer log files.
Skills required to participate
Python and structural neuroimaging experience. If one has experience with rdflib or PROV that would also be helpful. Any neuroanatomists in the audience? Would be helpful to have someone vet our mappings from atlas labels to anatomy terms.
Integration
This project will need expertise in programming, structural neuroimaging, and anatomy. To make this project sucessful we need individuals who have skills in any of these domains to help with: (1) understand Freesurfer's segmentation results format and log files; (2) programming up a script in Python; (3) understand anatomy well enough to select the proper anatomical concept that maps to a specific atlas designation of a region and can define new anatomy terms where needed, linking them to broader concepts to facilitate segmentation results queries across softwares.
Preparation material
Link to your GitHub repo
segstats_jsonld
with WIP ReadMe.md containing NOTE, this temporary github repo may change to be under ReproNim space
Communication
Haven't gotten this far yet but questions can be posted as issues in the GitHub repo linked above for via slack (@dbkeator) / mattermost (@dbkeator) / gmail (dbkeator@gmail.com)