Supplementary code to the manuscript: "Towards unconstrained compartment modeling in white matter using diffusion-relaxation correlation MRI with tensor-valued diffusion encoding" accepted in MRM 2020.
---Instructions for use---
- Clone this repository
- Clone the forked repository https://github.com/belampinen/md-dmri into a folder next to this repository.
- Run the script setup.m for setting up paths.
To process data according to in Lampinen et al (2020) MRM, run the script smr_process_example after changing the content under 'User provided details'. NB: the processing requires that Elastix (www.elastix.org) is installed.
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estimates: Parameter estimates for 15 subjects.
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figures: Code for creating Figures 2, 3 and 4, as well as Supporting Information Figures S1, S4 and S5
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model: Code for the two-compartment diffusion-relaxation model. Code for model fitting using the MDM framework (dtd_smr*)
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optimization: Protocol optimization based on the CRLB using SOMA. Run from smr_optimize_master.
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tools: Supporting functions used in various scripts.
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waveforms: The diffusion encoding waveforms used for the 'in vivo protocol'.
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dependencies: Additional necessary scripts