Hyperfine - Construction of isotropic image from tri-plane othogonal aquisitions

Overview

Usage

FAQ

Summary

Takes three orthogonally acquired images (axial, coronal, sagittal) collected on Hyperfine Swoop and combines into a single 1.5mm isotropic image.

Inputs:

• Axial
• Coronal
• Sagittal
• Template (age-matched) [now optional]

If no age matched template is provided, the algorithm will attempt to first make an initial template by rigid regisitration of all images to the axial plane. This will then be the reference for isotropic reconstruction. This has been tested with adult scans and shown comparable results to providing initial template.

There is now also a feature in the configuration to select if a phantom is being reconstructed.

Cite

license:

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

cite:

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.

• axi

  • Name: sxi
  • Type: file
  • Optional: false
  • Classification: file
  • Description: Axial plane acquisition

• sag

  • Name: sag
  • Type: file
  • Optional: false
  • Classification: file
  • Description: Sagital plane acquisition

• cor

  • Name: cor
  • Type: file
  • Optional: false
  • Classification: file
  • Description: Coronal plane acquisition }

Config

• template
  • Name: template
  • Type: string
  • Description: Volume template space (default: MNI152NLin2009cAsym)
  • Optional: true

Outputs

Isotropic volume

Metadata

No metadata currently created by this gear

Pre-requisites

• Three orthogonal aquisitions
• Age of participant (for age matched template)

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 ciso 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] --> FMI;
    FMI((file-metadata-importer)):::gear --> FC;
    FC((file-classifier)):::gear --> D2N;
    D2N((dcm2niix)):::gear --> CISO;
    CISO((ciso)):::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)
3. Select either a subject or a session.
4. Run the ciso 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.]