https://github.com/ucl/petmr-resolute
Implementation of RESOLUTE pseudo-CT method for mMR.
https://github.com/ucl/petmr-resolute
medical-imaging mrac pct pet-mr positron-emission-tomography
Last synced: 10 months ago
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Implementation of RESOLUTE pseudo-CT method for mMR.
- Host: GitHub
- URL: https://github.com/ucl/petmr-resolute
- Owner: UCL
- License: apache-2.0
- Created: 2018-02-27T16:22:44.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2018-08-21T23:00:44.000Z (almost 8 years ago)
- Last Synced: 2025-08-14T08:52:50.565Z (11 months ago)
- Topics: medical-imaging, mrac, pct, pet-mr, positron-emission-tomography
- Language: C++
- Size: 110 KB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# petmr-RESOLUTE
[](https://travis-ci.org/UCL/petmr-RESOLUTE) [](https://www.codacy.com/app/bathomas/petmr-RESOLUTE?utm_source=github.com&utm_medium=referral&utm_content=UCL/petmr-RESOLUTE&utm_campaign=Badge_Grade) [](https://zenodo.org/badge/latestdoi/123155931)
Implementation of the RESOLUTE pseudo-CT (pCT) method for the Siemens mMR.
If you use the RESOLUTE pCT approach in your work, please cite the following paper:
- Region specific optimization of continuous linear attenuation coefficients based on UTE (RESOLUTE): application to PET/MR brain imaging. Ladefoged, C. N., Benoit, D., Law, I., Holm, S., Kjaer, A., Hojgaard, L., … Andersen, F. L. (2015). Physics in Medicine and Biology, 60(20), 8047–8065. [DOI](https://doi.org/10.1088/0031-9155/60/20/8047)
## Required packages
- [ANTs](https://github.com/ANTsX/ANTs)
- [ITK](https://itk.org/) (Note. this can be built when compiling ANTs)
- [Boost](http://www.boost.org/)
- [glog](https://github.com/google/glog)
- [DCMTK](http://dicom.offis.de/). The application `dcmodify` must be available on your path.
## Template and mask images
The images that are required to run this application are available on Zenodo:
[](https://doi.org/10.5281/zenodo.1204196)
Please extract the zip and amend the JSON file as described below.
## Basic usage
```shell
./resolute -i -j
```
where `````` contains both the UTE and MRAC DICOM data for a given patient and `````` is the JSON configuration file. The application will produce a folder in the output directory specified in the JSON file. The output folder is named using the ```Study UID```, and inside this folder will be a new DICOM series comprising the RESOLUTE MRAC image.
## Configuration file
A skeleton JSON file can be created with the command:
```
./resolute --create-json
```
where `````` is an output filename.
The skeleton will look like this:
```yaml
{
"MRACSeriesName": "Head_MRAC_PET_UTE_UMAP",
"UTE1SeriesName": "Head_MRAC_PET_UTE",
"UTE1TE": "0.07",
"UTE2SeriesName": "Head_MRAC_PET_UTE",
"UTE2TE": "2.46",
"destDir": ".",
"destExportMethod": "FILE",
"destFileType": ".nii.gz",
"logDir": "./logs",
"regArgs": "3 -m CC[<%%REF%%>,<%%FLOAT%%>,1,4] -i 10x5x2 -o <%%PREFIX%%> -t SyN[0.5] -r Gauss[3,0] -G",
"regName": "ANTS",
"regTemplatePath": "",
"version": "0.0.1"
}
```
Fill in the desired output directory in the variable `destDir`, and the path to the registration template `manifest.json` in `regTemplatePath`, e.g.
```yaml
{
"MRACSeriesName": "Head_MRAC_PET_UTE_UMAP",
"UTE1SeriesName": "Head_MRAC_PET_UTE",
"UTE1TE": "0.07",
"UTE2SeriesName": "Head_MRAC_PET_UTE",
"UTE2TE": "2.46",
"destDir": "./OUTPUT",
"destExportMethod": "FILE",
"destFileType": ".nii.gz",
"logDir": "./logs",
"regName": "ANTS",
"regTemplatePath": "/path/to/template/manifest.json",
"regArgs": "3 -m CC[<%%REF%%>,<%%FLOAT%%>,1,4] -i 10x5x2 -o <%%PREFIX%%> -t SyN[0.5] -r Gauss[3,0] -G",
"version": "0.0.1"
}
```