NoddiSurfaceMapping

Optimized cerebral cortical surface mapping of neurite properties using diffsion magnetic resonace imaging (dMRI)

Example NODDI surface maps (NDI and ODI) compared with myelin and cortical thickness

Installation and Usage

1. Download NoddiSurfaceMapping.zip and unzip
2. Configure variables in the section of Setup in NoddiSUrfaceMapipng.sh depending on your local settings including AMICO. Note that you need to configure default settings of parallel diffusivity value in AMICO. By default, it is set to 1.7E-3 mm²/s but you need to change the value to 1.1E-3 mm²/s for NODDI cortical surface mapping (see Fukutomi et al., Neuroimage 2018).
3. Run NoddiSurfaceMapping.sh - inputs should be <StudyFolder> and <Subject directory(s)>, which were used to preprocess with HCP pipeline/DiffusionPreprocessing

 Calculate NODDI and do surface-mapping for HCP data
 Usage: NoddiSurfaceMapping <StudyFolder> <SubjectID 1> <SubjectID 2> ...
 
 Options:
     -a <num> : species atlas (0. Human [default], 1. Macaque, 2. Marmoset)
     -t <num>,<num>,<num> : b-value upper and lower threshold, and b=0 upper threshold (default: 3100,100,50)
     -M       : REGNAME=MSMAll (default: MSMSulc)
     -s       : do not calculate NODDI but only perform surface mapping

Dependencies

AMICO, HCP pipeline, Workbench, FSL

License

NoddiSurfaceMapping is licensed under the terms of the MIT license.

References

Fukutomi, H., Glasser, M.F., Zhang, H., Autio, J.A., Coalson, T.S., Okada, T., Togashi, K., Van Essen, D.C., Hayashi, T., 2018. Neurite imaging reveals microstructural variations in human cerebral cortical gray matter. Neuroimage. DOI BALSA