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https://github.com/cobralab/bsc

MRI biomarker, boundary sharpness coefficient (BSC).

https://github.com/cobralab/bsc

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

MRI biomarker, boundary sharpness coefficient (BSC).

Basic Info
  • Host: GitHub
  • Owner: CoBrALab
  • Language: Shell
  • Default Branch: main
  • Homepage:
  • Size: 39.1 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 5 years ago · Last pushed almost 5 years ago
Metadata Files
Readme

README.md

Description

Code for our newly developed MRI biomarker, boundary sharpness coefficient (BSC).

The BSC quantifies the transition between white matter and gray matter and is highly influenced by intracortical myelin. The proof-of-concept paper, written by Emily Olafson and others, is currently in available here : https://doi.org/10.1093/cercor/bhab015

Dependencies

  • minc-tool-kit 1.9.16(http://bic-mni.github.io/#v2-version-1918)
  • CIVET 2.1.0 (https://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET)
  • R 3.4.0
  • Rstudio
  • R-extras 3.4.0
  • RMINC (https://github.com/Mouse-Imaging-Centre/RMINC)
  • the R module mni.cortical.statistics (https://github.com/BIC-MNI/mni.cortical.statistics)
  • qbatch (https://github.com/pipitone/qbatch) but any tool for executing commands in parallel can be substituted (with modifications to run.sh)
  • Anaconda 5.1.0

Procedure

  1. Copy-paste 'setup_folders.sh' in the desired directory and run it
  2. Copy-paste 'run.sh' in main folder
  3. populate /methods with every file from this GitHub
  4. populate /scans with T1w volume in stereotaxic space (/final/IDt1tal.mnc in CIVET output)
  5. rename t1s so they fit the format : ID_t1.mnc
  6. populate surfaces/WM0surfaces with gray-white matter boundary surfaces in stereotaxic space (/surfaces/IDwhitesurfaceleft81920.obj and IDwhitesurfaceright81920.obj from CIVET output)
  7. rename whitesurfaces so they fit the format IDWM0surface_left.obj (same for right)
  8. populate surfaces/GM50surfaces with mid-surfaces in stereotaxic space (/surfaces/IDmidsurfaceleft81920.obj and IDmidsurfaceright81920.obj from CIVET output)
  9. rename midsurfaces so they fit the format IDGM50surface_left.obj (same for right)
  10. populate /surfmaps with surface maps transformations to surface model (/transforms/surfreg/IDleftsurfmap.sm and IDright_surfmap.sm from CIVET output)
  11. open 'run' and run the lines from the main folder, step by step (specific to CIC users)

Owner

  • Name: Computational Brain Anatomy Laboratory
  • Login: CoBrALab
  • Kind: organization
  • Email: contact@cobralab.ca
  • Location: Montreal, QC

Computational Brain Anatomy Laboratory, located in the CIC at the Douglas Institute, McGill University

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