This gear generates a DICOM from the isotropic reconstruction nifti data. Use axial DICOM as the reference dicom.

Usage

input = isotropic reconstruction (of nifti file to convert to dcm)
dcm = reference DICOM file
out = output filename
series = series number (optional)
desc = series description (optional)

FAQ

license: MIT License

url: https://github.com/Nialljb/fw-nii2dcm

cite:

Category: analysis

Gear Level:

• Project
• Subject
• Session
• Acquisition
• Analysis

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

• input
  • Base: file
  • Description: input file (isotropic reconstruction)
  • Optional: false

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

No metadata currently created by this gear

• Three dimensional structural reconstruction

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

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

This gear is run at either the Subject or the Session level. It downloads the data from the output of a previously run CISO analysis for that subject/session into the /flwyhweel/v0/work/ folder and then runs the nii2dcm pipeline on it.

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

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

A picture and description of the workflow

  graph LR;
    A[T2w]:::input --> FW;
    FW[FW] --> D2N;
    D2N((dcm2niix)):::gear --> CISO;
    CISO((recon)):::gear --> N2D;
    N2D[nii2dcm]:::container;
    
    classDef container fill:#57d,color:#fff
    classDef input fill:#7a9,color:#fff
    classDef gear fill:#659,color:#fff

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 nii2dcm

FAQ.md

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