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lampinen_mrm_2019

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---

  1. Clone this repository
  2. Clone the forked repository https://github.com/belampinen/md-dmri into a folder next to this repository.
  3. 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.

---FOLDER CONTENT----

  1. estimates: Parameter estimates for 15 subjects.

  2. figures: Code for creating Figures 2, 3 and 4, as well as Supporting Information Figures S1, S4 and S5

  3. model: Code for the two-compartment diffusion-relaxation model. Code for model fitting using the MDM framework (dtd_smr*)

  4. optimization: Protocol optimization based on the CRLB using SOMA. Run from smr_optimize_master.

  5. tools: Supporting functions used in various scripts.

  6. waveforms: The diffusion encoding waveforms used for the 'in vivo protocol'.

  7. dependencies: Additional necessary scripts