What is next in QMRITools

The main aim of the current roadmap is to optimize automatization of the processing and analysis pipelins. For this the BIDS dat structure is adoped and optimized for muscle also known as Muscle-Bids.

Currently the toobox allows processing from Dicom to merged fully processed datasets for T2-mapping, Dixon based imaging, and DTI/IVIM. Next steps will be muscle segentation and per muscle analysis of quantitative values and tractogrphy.

Upcomming code projects

Muscle faciculation analsyis

Optimize faciculation detection
Optimize faciculation analysis

Create common tensor space

Tensor align
- create methods for aligning between and within subject tensors
- registration based on distance maps
- registration based on tensor information
Muscle atlas cration

Tractography

create tract quantification and analysis tools
- muscle force line definitions
  - pennation anlge definitions
  - muscle to model files
  - tract deformations

Mask alignment

tools for mask homogenization
- Mask templating between subjects/cohorts

Muscle Bids

add MuscleBidsAnalysis
- Automated per muscle analysis once segmentation are present
add MuscleBidsQualityReport
add MuscleBidsAnalysisReport
add facicualtion analysis in MuscleBidsProcess

Muscle labeling

Related to muscle atlas project
- create muscle codes that lead to names and regions.
- add function to translate segmentation to muscle codes
  - will allow automated labeling for analysis
  - will allow grouping of segmentation in groups

Histology based simualations

If histology is availible allow diffusion simulations of cell segmentation
- based on the work of David Berry
- Allow parameterized generation of realistic muscle cells
- potentially add internal muscle organells