https://github.com/mercure-imaging/mercure-dcm2bids

Module to run dcm2bids conversion in mercure.
https://github.com/mercure-imaging/mercure-dcm2bids

Last synced: about 2 months ago
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Module to run dcm2bids conversion in mercure.

• Host: GitHub
• URL: https://github.com/mercure-imaging/mercure-dcm2bids
• Owner: mercure-imaging
• License: gpl-3.0
• Created: 2023-11-16T17:08:30.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-01-26T13:52:06.000Z (8 months ago)
• Last Synced: 2024-06-20T23:55:32.895Z (3 months ago)
• Language: Jupyter Notebook
• Size: 2.06 MB
• Stars: 0
• Watchers: 0
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bids - mercure-dcm2bids - source DICOM orchestration platform that can integrate containerized apps into clinical workflows. It has a graphical user interface making it easy to setup and manage BIDS configurations for multiple protocols. The Dcm2Bids tool is used for conversion. (Converters / MRI)

README

        
# **mercure-dcm2bids**




Mercure module to perform DICOM to BIDS conversion using the [dcm2bids](https://github.com/UNFmontreal/Dcm2Bids) converter. dcm2bids reorganises NIfTI files using dcm2niix into the Brain Imaging Data Structure (BIDS). This module runs as a docker container in mercure, it can be added to an existing mercure installation using docker tag : *mercureimaging/mercure-dcm2bids*. The BIDS configuration .json content can be entered directly into the settings tab in the *Rules* or *Modules* pages of mercure's web-based interactive user interface. The module will generate a .zip file of the BIDS directory structure created using the dcm2bids scaffolding, including the original DICOM files in the *sourcedata* directory and converted BIDS data (see [dcm2bids documentation](https://unfmontreal.github.io/Dcm2Bids) for further details on the scaffold directory structure).




## **Installation**

### Add module to existing mercure installation

Follow instructions on [mercure website](https://mercure-imaging.org) on how to add a new module. Use the docker tag *mercureimaging/mercure-dcm2bids*.




### Build module for local testing, modification and development

1. Clone repo.

2. Build Docker container locally by running make (modify makefile with new docker tag as needed).

3. Test container :\

`docker run -it -v /input_data:/input -v /output_data:/output --env MERCURE_IN_DIR=/input  --env MERCURE_OUT_DIR=/output mercureimaging/mercure-dcm2bids`




### Quick start tutorial

Follow the ['First steps' tutorial](https://github.com/mercure-imaging/mercure-dcm2bids/blob/main/mercure_dcm2bids_first_steps_tutorial.ipynb) and setup an end-to-end mercure test environment for BIDS conversion on your local machine. The tutorial provides simple steps to guide installation of mercure with the mercure-dcm2bids module, and then to perform a BIDS conversion using a test DICOM dataset. It takes about one hour to complete.




## **Configuration**

### Define output directory in *Targets* page in mercure

The mercure-dcm2bids module requires an output directory for the zipped converted data. See example in image below for '/vagrant' directory. Click *test* button to ensure mercure can write to specified directory







![image](target.png)







### Add BIDS configuration file content 

The BIDS configuration for a project can be added to the 'Settings' tab in either the *Modules* or *Rules* pages. Adding the .json content to *Rules* is preferred to allow multiple BIDS configurations to coexist and run with a single dcm2bids module. More information on mercure rule configuration can be found [here](https://mercure-imaging.org/docs/usage.html#defining-rules). An example BIDS configuration based on the dcm2bids [first steps tutorial](https://unfmontreal.github.io/Dcm2Bids/docs/tutorial/first-steps/) is shown in the screenshot below.







![image](config.png)







Full configuration .json text for the first steps example:

~~~

{

  "descriptions": [

    {

      "id": "id_task-rest",

      "datatype": "func",

      "suffix": "bold",

      "custom_entities": "task-rest",

      "criteria": {

        "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*"

      },

      "sidecar_changes": {

        "TaskName": "rest"

      }

    },

    {

      "datatype": "fmap",

      "suffix": "epi",

      "criteria": {

        "SeriesDescription": "EPI PE=*"

      },

      "sidecar_changes": {

        "intendedFor": ["id_task-rest"]

      }

    }

  ]

}

~~~




## **dcm2bids project**

### Information

Documentation: https://unfmontreal.github.io/Dcm2Bids/latest/

Ideas/New features: https://github.com/UNFmontreal/Dcm2Bids/issues

Questions/Issues: https://neurostars.org/tag/dcm2bids




### Acknowledgments

~~~

Boré, A., Guay, S., Bedetti, C., Meisler, S., & GuenTher, N. (2023). Dcm2Bids (3.1.1). Zenodo. https://doi.org/10.5281/zenodo.8436509

~~~