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https://github.com/reubendo/remind
Scripts used for the conversion of the NRRD data to DICOM data
https://github.com/reubendo/remind
Last synced: about 2 months ago
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Scripts used for the conversion of the NRRD data to DICOM data
- Host: GitHub
- URL: https://github.com/reubendo/remind
- Owner: ReubenDo
- License: mit
- Created: 2023-06-12T18:17:56.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-12-11T18:46:36.000Z (about 1 year ago)
- Last Synced: 2023-12-11T19:32:33.732Z (about 1 year ago)
- Language: Python
- Size: 16.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ReMIND Data Conversion Scripts
This repository includes scripts designed for the conversion of ReMIND data between NRRD and DICOM formats. The scripts serve two primary purposes:
1. **Conversion from NRRD to DICOM for TCIA:**
- Step 1: Conversion of NRRD images to DICOM images for ultrasound and MR data.
- Step 2: Conversion of NRRD SEG to DICOM SEG for segmentation files.
2. **Conversion of TCIA Imaging Data from DICOM to NRRD:**
- Convert DICOM imaging data downloaded from TCIA into NIfTI or NRRD formats.
## Example Output
Below is an example of a DICOM folder loaded in 3D Slicer:
## Conversion from NRRD to DICOM for TCIA
### Step 1: Conversion of NRRD images to DICOM images
- Ultrasound images are converted using the [Dicom3tools software](https://www.dclunie.com/dicom3tools.html) as multi-frame DICOM files.
- MR data is converted using [3D Slicer](https://download.slicer.org/).
#### Requirements
1. Java: Download from [here](https://www.oracle.com/java/technologies/downloads/)
2. 3D Slicer: Download from [here](https://download.slicer.org/)
#### Command
On MacOS:
```bash
/Applications/Slicer.app/Contents/MacOS/Slicer --no-splash --python-script conversion_imaging.py --path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom
```
On Windows:
```bash
Slicer.exe --no-splash --python-script nrrd_to_dicom_img.py --path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom
```
### Step 2: Conversion of NRRD SEG to DICOM SEG
NRRD segmentation files are converted with dcmqi using DICOM images as a reference.
#### Requirements
1. dcmqi: binaries for your operating system are available [here](https://qiicr.gitbook.io/dcmqi-guide/opening/installation/binary_packages)
#### Command
To process segmentations:
```python nrrd_to_dicom_seg.py--path_nrrd [PATH_TCIA_NRRD] --path_dicom ./dicom --img2seg ../dcmqi-1.2.4-mac/bin/itkimage2segimage```
# Conversion of the imaging data from DICOM to NRRD
To convert DICOM imaging data downloaded from TCIA into NIfTI or NRRD formats, follow these guidelines:
#### Requirements
1. Download imaging data from [TCIA](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=157288106)
2. Python with the required packages (install with ```pip install -r requirements.txt```)
#### Command
To convert DICOM images into NIfTI format:
```python dicom_to_nifti-nrrd_img.py --path_dicom [PATH_REMIND_DATA] --nifti ```
To convert DICOM images into NRRD format:
```python dicom_to_nifti-nrrd_img.py --path_dicom [PATH_REMIND_DATA] --nrrd ```
Replace `[PATH_REMIND_DATA]` with the path to the downloaded ReMIND imaging data (e.g., `data/ReMIND_TCIA/manifest-1695134609823/ReMIND/`).