Diffusion and Displacement Encoded MRI Dataset to Estimate In Vivo Cardiomyocyte Strain

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Submitted by:
Ilya Verzhbinsky
Last updated:
Tue, 05/17/2022 - 22:17
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Changes in left ventricular (LV) aggregate cardiomyocyte  orientation and deformation underlie cardiac function and dysfunction. As such, in vivo aggregate cardiomyocyte "myofiber" strain has mechanistic significance, but currently there exists no established technique to measure in vivo cardiomyocyte strain.


The following dataset contains Dispalcement Encoding with Stimulated Echoes (DENSE) MRI and cardiac Diffusion Tensor Imaging (cDTI) data. The functional data from DENSE MRI along with the microstructural data reconstructed from cDTI can be used to compute strain along the cardiomyocyte axis. 



## Supplemental MRI Data for in vivo estimation of cardiomyocyte strain ##


The contents of this dataset includes the necessary DENSE MRI and cDTI data to 

compute in vivo cardiomyocyte strain at one mid-ventricular location. The 

following README file will break down the contents of this supplemental dataset.


A detailed description of the methods used to compute cardiomyocyte strain from

the attached data can be found in the following work:


> Verzhbinsky, I.A., Perotti, L.E., Moulin K., Cork, T.E., Loecher, M., 

> Ennis, D.B. (2019). Estimating Aggregate Cardiomyocyte Strain Using In Vivo 

> Diffusion and Displacement Encoded MRI. 



### DENSE folder


#### Dicom subfolder

The DENSE folder contains all DENSE MRI data in the 'Dicom' subfolder. Data is 

divided into magnitude, x phase, y phase, and z phase dicoms for 2 DENSE MRI

slices located 4 mm above and below the location of cDTI.


#### Processed subfolder

The 'Processed' subfolder contains the processed Langrangian displacements for 

each DENSE MRI slice in a MatLab file format. DENSE MRI displacement data was 

processed using the following open-source DENSE processing tool:


> https://github.com/denseanalysis/denseanalysis



### cDTI folder


#### Dicom subfolder

Diffusion weighted dicom data acquired across the entire left ventricle is 

located in the Dicom subfolder. The data is organized into 1 b0 image followed

by 12 diffusion weighted images repeated 30 times. 


(1 b0 + 12 Diffusion) * 30 averages = 390 total images.  


The cDTI slice that is located between the 2 provided DENSE slices is number 6, 

with image number 1 beginning at the most apical slice.


### Processed subfoler

The processed subfolder contains a single MatLab file with the diffusion weighed

images and reconstructed diffusion tensors registered to the DENSE MRI data. 


'IMaffine' - a cDTI image matrix at slice 6 with the following dimensions:

[yres xres (b0 + 12 diffusion)]


'D' - the registered reconstructed diffusion tensors at slice 6 with the 

following dimensions:

[yres xres 3 3] 

At each cDTI voxel, all reconstructed diffusion tensors are represented as 

symmetric 3 by 3 matrices.