nialljb / fw-ants-vbm

ANTs VBM

This gear performs Voxel Based Morophometry using Jacobian determinants with ANTs on infants between 0-2 years old with isotropic reconstructed Hyperfine scans.

Overview

Usage Should be automated if setup correctly. Requires age to select appropriate template for registration. The configuration allows a selection of atlases to choose from. ROI volume estimation will be performed on these. FAQ

Summary

Takes the isotropic hyperfine reconstructions that have been bias corrected (N4) and calculates volume estimates for white matter, grey matter & CSF by calculating Jacobian determinants.

• Requires matching to template used in recon
• Required brain mask from HD-BET (Could include conditional to run HD-BET if files not found)

Cite

license: MIT License

url: https://github.com/Nialljb/fw-ants-vbm

cite:
Sean C.L. Deoni, Muriel M.K. Bruchhage, Jennifer Beauchemin, Alexandra Volpe, Viren D'Sa, Matthew Huentelman, Steven C.R. Williams, Accessible pediatric neuroimaging using a low field strength MRI scanner, NeuroImage, Volume 238, 2021, 118273, ISSN 1053-8119, https://doi.org/10.1016/j.neuroimage.2021.118273.
(https://www.sciencedirect.com/science/article/pii/S1053811921005498)

Bourke, N. J., Demarchi, C., De Simoni, S., Samra, R., Patel, M. C., Kuczynski, A., Mok, Q., Wimalasundera, N., Vargha-Khadem, F., & Sharp, D. J. (2022). Brain volume abnormalities and clinical outcomes following paediatric traumatic brain injury. Brain, 145(8), 2920\u20132934. https://doi.org/10.1093/brain/awac130

Classification

Category: analysis

Gear Level:

• Project
• Subject
• Session
• Acquisition
• Analysis

---

Inputs

• api-key
  • Name: api-key
  • Type: object
  • Optional: true
  • Classification: api-key
  • Description: Flywheel API key.

Config

• input
  • Base: file
  • Description: input file (isotropic reconstruction, bias corrected & skull stripped)
  • Optional: false

Outputs

• output

  • Base: file
  • Description: segmentated file
  • Optional: false

• volume

  • Base: file
  • Description: volume estimation file (csv)
  • Optional: true

Metadata

No metadata currently created by this gear

Pre-requisites

• Three dimensional structural image, bias corrected and skull stripped

Prerequisite Gear Runs

1. dcm2niix
   • Level: Any
2. file-metadata-importer
   • Level: Any
3. file-classifier
   • Level: Any

Prerequisite

Usage

This section provides a more detailed description of the gear, including not just WHAT it does, but HOW it works in flywheel

Description

This gear is run at either the Subject or the Session level. It downloads the data from the output of a previously run HD-BET analysis for that subject/session into the /flwyhweel/v0/work/ folder and then runs the hyperfine-vbm pipeline on it.

After the pipeline is run, the output folder is zipped and saved into the analysis container.

File Specifications

This section contains specifications on any input files that the gear may need

Workflow

A picture and description of the workflow

  graph LR;
    A[T2w]:::input --> FW;
    FW[FW] --> D2N;
    D2N((dcm2niix)):::gear --> CISO;
    CISO((recon)):::gear --> N4;
    N4((biasCorr)):::gear --> BET;
    BET((HD-BET)):::gear --> VBM;
    VBM[Morphometry]:::container;
    
    classDef container fill:#57d,color:#fff
    classDef input fill:#7a9,color:#fff
    classDef gear fill:#659,color:#fff

Loading

Description of workflow

1. Upload data to container
2. Prepare data by running the following gears:
   1. file metadata importer
   2. file classifier
   3. dcm2niix
3. Run the ciso gear (Hyperfine triplane aquisitions)
4. Run N4 bias correction gear
5. Run HD-BET
6. Run VBM

Use Cases

FAQ

FAQ.md

Contributing

[For more information about how to get started contributing to that gear, checkout CONTRIBUTING.md.]