SVRTK

UNDER DEVELOPMENT

Wrapper for Flywheel gear: slice to volume reconstruction toolkit

Source: https://github.com/SVRTK/SVRTK

Overview

Usage

FAQ

Summary

Cite

license:

url: https://gitlab.com/flywheel-io/flywheel-apps/

cite:
Uus, A., Grigorescu, I., van Poppel, M., Steinweg, J. K., Roberts, T., Rutherford, M., Hajnal, J., Lloyd, D., Pushparajah, K. & Deprez, M. (2022) Automated 3D reconstruction of the fetal thorax in the standard atlas space from motion-corrupted MRI stacks for 21-36 weeks GA range. Medical Image Analysis, 80 (August 2022).: https://doi.org/10.1016/j.media.2022.102484

Kuklisova-Murgasova, M., Quaghebeur, G., Rutherford, M. A., Hajnal, J. V., & Schnabel, J. A. (2012). Reconstruction of fetal brain MRI with intensity matching and complete outlier removal. Medical Image Analysis, 16(8), 1550–1564.: https://doi.org/10.1016/j.media.2012.07.004

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

• debug

  • Name: debug
  • Type: boolean
  • Description: Log debug messages
  • Default: false

• input

  • Base: file
  • Description: input file
  • Optional: false

Outputs

• output
  • Base: file
  • Description: file
  • Optional: false

Metadata

No metadata currently created by this gear

Pre-requisites

• Three dimensional structural image

Prerequisite Gear Runs

This gear runs on BIDS-organized data. To have your data BIDS-ified, it is recommended that you run, in the following order:

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 for that subject/session into the /flwyhweel/v0/work/bids folder and then runs the synthseg 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[T1w]:::input --> FW;
    FW[FW] --> FMI;
    FMI((file-metadata-importer)):::gear --> FC;
    FC((file-classifier)):::gear --> D2N;
    D2N((dcm2niix)):::gear --> CB;
    CB((curate-bids)):::gear --> CISO;
    svrtk((svrtk)):::gear --> SS;
    SS((synthseg)):::gear --> ANA;
    ANA[Analysis]:::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
   4. MRIQC (optional)
   5. curate bids
3. Select either a subject or a session.
4. Run the svrtk-brain-reconstruction gear
5. Gear places output in Analysis

Use Cases

FAQ

FAQ.md

Contributing

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