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README.md

Tutorial about tensor reconstruction and reorientation using the NC_EPI3D_DIFF sequence

Here is a brief tutorial for tensor reconstruction and reorientation using the NC_EPI3D_DIFF sequence. Largely inspired from https://github.com/ANTsX/ANTs/wiki/Warp-and-reorient-a-diffusion-tensor-image. The NC_EPI3D_DIFF sequence has been developped by Dr. Nadege Corbin, CNRS, Bordeaux.

Acknowledgments

The author is grateful for the help provided via the Github or Discourse platform by Philip Cook and Nick Tustison regarding the use of ANTs and Max Pietsh, Robert Smith and Donald Tournier regarding the use of MRtrix3 software.

References

Here are relevent references for this script in cardiac DTI:

Cabanis, P., Magat, J., Rodriguez-Padilla, J., Ramlugun, G., Yon, M., Bihan-Poudec, Y., ... & Ozenne, V. (2023). Cardiac structure discontinuities revealed by ex-vivo microstructural characterization. A focus on the basal inferoseptal left ventricle region. Journal of Cardiovascular Magnetic Resonance, 25(1), 78.

Rodriguez Padilla J, Petras A, Magat J, Bayer J, Bihan-Poudec Y, El-Hamrani D, Ramlugun G, Neic A, Augustin C, Vaillant F, Constantin M, Benoist D, Pourtau L, Dubes V, Rogier J, Labrousse L, Bernus O, Quesson B, Haissaguerre M, Gsell M, Plank G, Ozenne V, Vigmond E. Impact of Intraventricular Septal Fiber Orientation on Cardiac Electromechanical Function. Am J Physiol Heart Circ Physiol. 2022 Mar 18. doi: 10.1152/ajpheart.00050.2022. Epub ahead of print. PMID: 35302879.

Magat J, Yon M, Bihan-Poudec Y, Ozenne V (2022) A groupwise registration and tractography framework for cardiac myofiber architecture description by diffusion MRI: An application to the ventricular junctions. PLOS ONE 17(7): e0271279. https://doi.org/10.1371/journal.pone.0271279

Environnement

ANTs and MRtrix are mandatory dependencies. ITK-SNAP and 3DSlicer may be usefull as well.

OS version

Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.2 LTS
Release:	22.04
Codename:	jammy

MRtrix version

valery:~/Dev/Cardiac-Structure-Database$ `mrcalc`` --version
== mrview 3.0.3-98-gb3409159 ==
64 bit release version, built Apr 20 2022, using Eigen 3.3.7
Author(s): J-Donald Tournier ([email protected]), Dave Raffelt ([email protected]), Robert E. Smith ([email protected]), Rami Tabbara ([email protected]), Max Pietsch ([email protected]), Thijs Dhollander ([email protected])
Copyright (c) 2008-2022 the MRtrix3 contributors.

ANTs version

valery:~/Dev/Cardiac-Structure-Database$ `antsRegistration`` --version
ANTs Version: v2.3.5.post106-gd0156d3
Compiled: Apr 20 2022 11:20:40

MRI

The NC_EPI3D_DIFF is available via CPP on all VE versions of Siemens MRI. It has been mainly tested on 3T Prisma and Skyra. Please contact Nadege Corbin for further information.

Context

6 DWI sequences has been acquired on ex vivo sample and are accesible at this "https://mille-feuilles.ihu-liryc.fr/#collection/666afd6021199c3aab754796/folder/678f9e409332b35e6e4dafbf".

Acquisitions were performed with Lucy Kershaw from Centre for Cardiovascular Science and Edinburgh Imaging Facilities and John Keen from The Royal School of Veterinary Studies and The Roslin Institute.

Information must be set in a separate json files in Jsons/. It assummes single shell (here b=1000). b0 acquisitions in RL/LR or PA/AP has been acquired. TopUp correction and N4Bias correction are not presented here.

Code

A code for the computation and reorientation of the diffusion tensor metric is avaible. Jsons file are used to set the DICOM folder name and path in the Jsons folder. The code is subject to change at any moment. As an example, the code automatically produces the following figures.

The code combine the use of MRtrix for diffusion metric estimation and ANTs for reorientation. Please run either run_all.sh or

./command_extract_tensor.sh ../Jsons/Acquisition1.json

A crucial step is the tensor conversion from MRtrix to ANTs format. Two subscripts are in charge of such task. Please check that /tmp/ folder exist and we have permission in this folder.

Additionnal feature have been developped and could be added upon request.

  • TopUp correction
  • N4Biais correction
  • Generation of streamlines
  • Reorientation of streamlines.
  • Non-linear registration of samples
  • Atlas / Template approaches for ex-vivo sample hearts.
  • Angles, myocardial disarray index calculation

Notes

Note that high intensity signal is present in the mean b0 images leading to apparent black signal, cut off fix the display issue.

Jsons

{
    "sequence": [
 
       {  "PROJECT_FOLDER":"/workspace_QMRI/PROJECTS_DATA/2025_RECH_EPI3Ddiff_horse/",
          "MAIN_EXAM_FOLDER_NAME":"0115_HORSEHEART_25_01_15-11_43_10-STD-1_3_12_2_1107_5_2_43_66056",
          "SUB_EXAM_FOLDER_NAME": "RMSB_PC_20250115_114338_281000",
          "MRTRIX_FOLDER_NAME":"Mrtrix_Reco_3_RL_seg4_8dir_2.0mm",
          "DIR": 8,
          "BVALUE": 1000,
          "SEQ_AP_B0_FOLDER_NAME": "NC_EPI3D_DIFF_S4_B0_OBL_RL_0007",         
          "SEQ_PA_B0_FOLDER_NAME": "NC_EPI3D_DIFF_S4_B0_OBL_LR_0008",
          "SEQ_AP_BVALUE_FOLDER_NAME": "NC_EPI3D_DIFF_S4_B1000_OBL_RL_0009",         
          "MPRAGE_FOLDER": "3DT1_MPRAGE_0005", 
          "TRANSFORM_ALIGNED": "1/transform_itk_native_to_LA.txt",
          "RESLICED_REFERENCE": "1/resliced_volume_in_LA_space_2.0mm.nii.gz",
          "THRESHOLD":30,
          "FORCE": "0"
       }      
    ]
}

Figures

Sample after reorientation

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