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Left atrial flattening

Author: Marta Nuñez-Garcia (marnugar@gmail.com)

About

Implementation of the Left Atrial (LA) Fast Regional Flattening (FRF) method described in: Fast quasi-conformal regional flattening of the left atrium. Marta Nuñez-Garcia, Gabriel Bernardino, Francisco Alarcón, Gala Caixal, Lluís Mont, Oscar Camara, and Constantine Butakoff. IEEE Transactions on Visualization and Computer Graphics (2020). Please cite this reference when using this code. Preprint available at: arXiv:1811.06896. The code runs in Linux and Windows.

Example:

Example image

Code

Python scripts depending (basically) on VTK and VMTK.

Pipeline

The pipeline is split in 4 parts. You can skip the first ones depending on your input data.

  • 1_mesh_standardisation: standardises LA mesh, i.e. clip pulmonary veins (PVs), left atrial appendage (LAA), and mitral valve (MV). Launches GUI and asks the user to select 5 seeds close to the ending points of the 4 PVs and LAA. It returns a clipped mesh and auxiliary files containing info about seeds, clipping planes, etc. This script is adapted from run_standardization by Catalina Tobon Gomez.
  • 2_close_holes_project_info: Closes holes corresponding to clipped PVs and LAA. Hole filling is done with Butakoff's implementation of the method published in P. Liepa "Filling Holes in Meshes", 2003. The binary file is included in this repository, you may need to provide execution permission (chmod +x FillSurfaceHoles). Hole filling can also be done manually with reMESH. This script also marks the filled holes with a scalar array and additionally, transfers all scalar arrays in the input mesh to the output (closed) mesh.
  • 3_divide_LA: Parcellates mesh creating appropriate paths to divide the LA in the 5 pieces considered in our regional flattening. Launch GUI and ask the user to select the 9 required seeds. See seeds order here: Example image
  • 4_flat_atria: Quasi-conformal LA regional flattening. Given a LA mesh with clipped & filled holes (PVs, LAA) and only 1 hole corresponding to the MV, it returns a flat (2D) version of the input mesh. Implementation of a conformal flattening considering 6 boundaries (4 PVs + LAA + MV) and the additional regional constraints (division lines) obtained in the previous step.

Instructions

Clone the repository:

git clone https://github.com/martanunez/LA_flattening

cd LA_flattening

Usage

1_mesh_standardisation.py [-h] [--meshfile PATH] [--pv_dist PV_DIST]
                                 [--laa_dist LAA_DIST] [--maxslope MAXSLOPE]
                                 [--clspacing CLSPACING]
                                 [--skippointsfactor SKIPPOINTSFACTOR]
                                 [--highslope HIGHSLOPE]
                                 [--bumpcriterion BUMPCRITERION]
                                 [--pvends PVENDS] [--vis VIS] [--save SAVE]

Arguments:
  --meshfile PATH       path to input mesh

Optional arguments:
  -h, --help            show this help message and exit
  --pv_dist PV_DIST     PV clipping distance (mm)
  --laa_dist LAA_DIST   LAA clipping distance (mm)
  --maxslope MAXSLOPE   Anything above this is ostium
  --clspacing CLSPACING
                        Resample the centerline with this spacing
  --skippointsfactor SKIPPOINTSFACTOR
                        Percentage of points to ignore at beginning of centerline
  --highslope HIGHSLOPE
                        Above this slope we start counting
  --bumpcriterion BUMPCRITERION
                        Ostium if slope higher than highslope and above bump criterion
  --pvends PVENDS       Enforce the centerline to reach the end boundary of the surface.
  --vis VIS             Set to 1 to visualise clipping results overlaid with original mesh
  --save SAVE           Set to 0 to remove intermediate results (centerlines, clippoints, etc.)
____________________________________________________________________________

2_close_holes_project_info.py [-h] [--meshfile_open PATH]
                                     [--meshfile_open_no_mitral PATH]
                                     [--meshfile_closed PATH]

Arguments:
  -h, --help            show this help message and exit
  --meshfile_open PATH  path to input mesh with clipped PVs and LAA
  --meshfile_open_no_mitral PATH
                        path to input mesh with additional MV clip
  --meshfile_closed PATH
                        path to output mesh, i.e. with filled holes
____________________________________________________________________________

usage: 3_divide_LA.py [-h] [--meshfile PATH]

Arguments:
  -h, --help       show this help message and exit
  --meshfile PATH  path to input mesh
___________________________________________________________________________

usage: 4_flat_atria.py [-h] [--meshfile PATH] [--save_conts SAVE_CONTS]
                       [--save_final_paths SAVE_FINAL_PATHS]

Arguments:
  --meshfile PATH       path to input mesh
  
Optional arguments:
  -h, --help            show this help message and exit
  --save_conts SAVE_CONTS
                        set to true to save mesh contours/contraints
  --save_final_paths SAVE_FINAL_PATHS
                        set to true to save modified dividing paths

Usage example

python 1_mesh_standardisation.py --meshfile data/mesh.vtk --pv_dist 5 --laa_dist 5 --vis 1

python 2_close_holes_project_info.py --meshfile_open data/mesh_crinkle_clipped.vtk --meshfile_open_no_mitral  data/mesh_clipped_mitral.vtk --meshfile_closed data/mesh_clipped_c.vtk

python 3_divide_LA.py --meshfile data/mesh_clipped_c.vtk

python 4_flat_atria.py --meshfile data/mesh_clipped_c.vtk

Dependencies

The scripts in this repository were successfully run with:

  1. Ubuntu 16.04

  2. Ubuntu 16.04

  3. Windows 8.1

Other required packages are: NumPy, SciPy, xlsxwriter, Matplotlib, joblib, and python-tk.

Python packages installation

To install VMTK follow the instructions here. The easiest way is installing the VMTK conda package (it additionally includes VTK, NumPy, etc.). It is recommended to create an environment where VMTK is going to be installed and activate it:

conda create --name vmtk_env
conda activate vmtk_env

Then, install vmtk:

conda install -c vmtk vtk itk vmtk

Nevertheless, for Ubuntu, the easiest option for me was to build VMTK from source (slowly but surely). Instructions can be found here. In brief:

git clone https://github.com/vmtk/vmtk.git
mkdir vmtk-build
cd vmtk-build
ccmake ../vmtk
make 

And edit the ~/.bashrc file,

gedit ~/.bashrc

adding the following line: source /home/{your_path_to_vmtk}/vmtk/vmtk-build/Install/vmtk_env.sh

Important note

You may need to slightly modify vmtkcenterlines.py from the VMTK package if you encounter the following error when running 1_mesh_standardisation.py:

     for i in range(len(self.SourcePoints)/3):
TypeError: 'float' object cannot be interpreted as an integer

Find vmtkcenterlines.py file and edit as follows:

Line 128: change for i in range(len(self.SourcePoints)/3): by for i in range(len(self.SourcePoints)//3):

Line 133: change for i in range(len(self.TargetPoints)/3): by for i in range(len(self.TargetPoints)//3):

License

The code in this repository is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details: http://www.gnu.org/licenses/

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Implementation of quasi-conformal regional flattening of the left atrium

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