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A library to calculate parametric maps in MRI. For details see https://doi.org/10.1016/j.softx.2019.100369

License: Other

CMake 2.67% C++ 93.19% Shell 0.87% MATLAB 0.27% Python 2.96% C 0.03%

mri itk t1 parametric-mapping cardiac shmolli molli

tomato's Introduction

Based on: Github Repository

License

The MIT License (MIT)

Copyright (c) 2015 Dragomir V Yordanov

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

tomato's People

Contributors

Stargazers

Watchers

Forkers

elseviersoftwarex iuliapopescu jamie-roberts

tomato's Issues

Main executable does not get built (Linux)

I am trying to compile your tool for use on a Linux cluster
Unfortunately, even if I specify BUILD_APP=ON in cmake, the main executable (app/main.cpp) does not get built.
Please, would you have any advice?

I'm builing Tomato on

CentOS Linux release 7.9.2009
gcc/g++ 4.9.4
cmake version 3.22.1

Thanks

Installation Instructions

Looks like an interesting suite of tools! Do you have installation/build instructions or should you just use one of the releases? I think it'd be good to include this in the README.

Shmolli discrepancies

Tomato's way of calculating Shmolli T1 gives 1ms different results than Shmolli original. As Fitting method is identical, I believe that the discrepancies come from the cost calculation.

implement and compare 'last fitted value'
extract fitting function from the original and compare it with Tomato's

5 samples calculation time

5 samples calculation time seems to be way longer than 7 samples. Why?

implement calculation time map to identify problematic pixels

itkReadDirectory correct invTimes

make itkReadDirectory to be able to read invTimes similarly to itkReadFileListFilter

Self contained lib package for the releases

add itk, lmfit and other pre-compiled libs to the TomatoLib distribution

TomatoExe: when input is in form of a directory, dicom tags of the output are not being filled

When the input is in form of a directory in the yaml file, dicom tags like patient name in the output are not being filled

Idea: One pixel executable

The executable could take 3 files as arguments:

Config file
Input data file

invTimes
mag
pha
timesSeries - to calculate values from the model

Output results file

results
model results

Deploy pure TomatoLib dll's and so's

Add compilation to a mex

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