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MP3 a medical imaging toolbox (MRI, CT, PET...)

version 1.3 (158 MB) by benjamin lemasson
Medical software for Processing multi-Parametric images Pipelines

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Updated 22 Jul 2020

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Medical software for Processing multi-Parametric images Pipelines

More information available in our publication (https://www.frontiersin.org/articles/10.3389/fninf.2020.594799/full):
MP3: Medical software for Processing multi-Parametric images Pipelines.
Brossard el al.; Frontiers in Neuroinformatics, 2020, 14, 53.

Presentation and tutorials are available here !
https://www.youtube.com/playlist?list=PL-Tj6Wc9aE9x7i6s-RLetvNE0isnEsFm7

MP³ is an open source software aimed to support preclinical and clinical researchers for image processing studies. This Matlab toolbox offers a graphical interface that helps to process medical images. Here are the most important tools included in MP³ :

Import medical images (e.g. DICOM, NIFTI, Bruker, …) and convert them to nifti/json format
Visualize images (2D to 5D data)
Process (e.g. registration, model fit, filters, …)
Analyze (e.g. ROIs, scatterplots, …) medical images.
Standard processes from SPM or FSL can be called as well as custom fonctions. Complex postprocessing pipelines can be created and applied to mutiparametric (e.g. MRI T1w + MRI T2w,…), multidimensional (e.g. spatial +temporal+echoes,…) or multimodal (e.g. MRI +CT, …) data. Once defined in a single patient, these processes can be stored and applied to a larger database using parallel architectures. MP³ was initially created in the Grenoble Institute of Neurosciences (France) to process multiparametric MRI protocols (anatomy+relaxometry+perfusion) in cohorts of +500 animals.

SUMMARY Poster (ENGLISH) (FRENCH): poster presented at the 4th Congress of the SFRMBM (Strasbourg).

Requirements
In order to fully enjoy MP³, you have to meet the following requirements:

Matlab 2017b or higher
Toolboxes (Mandatory : Image Processing Toolbox -- Recommended : Statistics and Machine Learning Toolbox ; Parallel Computing Toolbox)
Java 8 or higher
Data to process in Bruker / DICOM / Philips / Nifti format

This project is developed in the Grenoble Institut of Neurosciences by the team Neuroimaging and brain perfusion
The main contributors of this project are : Clément Brossard and Benjamin Lemasson

keys words : animal, ants, asl, brain extraction, bruker, cbv, clinical, clustering, compute tomography, conversion, ct, database, dicom, fit, fsl, human, image analysis, image processing, image registration, mask, mouse, mri, multiparametric, parrec, perfusion, pipeline, preclinical, radiomic, radiomics, rat, so2, spm, t1, T2, T2*, vsi

Cite As

benjamin lemasson (2021). MP3 a medical imaging toolbox (MRI, CT, PET...) (https://github.com/nifm-gin/MP3/releases/tag/v1.3), GitHub. Retrieved .

Brossard, C., Montigon, O., Boux, F., Delphin, A., Christen, T., Barbier, E. L., & Lemasson, B. (2020). MP3: Medical software for Processing multi-Parametric images Pipelines. Frontiers in Neuroinformatics, 14, 53.

Comments and Ratings (10)

wafae labriji

Justine Deborne

Jenita Subash

Matthieu Doyen

Excellent toolbox, many functionalities are useful, thanks. I used it to create my ROI on MRI images, generate my parametric maps and interpret my results (clustering). The pipeline process is smart and easy to use.

Max

Aurelien Delphin

Stenzel CACKOWSKI

Fabien Boux

Clément Brossard

Veronica Munoz

MATLAB Release Compatibility
Created with R2017b
Compatible with R2017b and later releases
Platform Compatibility
Windows macOS Linux

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MP3_pipeline

MP3_pipeline/Modules/Modules_Furnished/DatabaseUtilities

MP3_pipeline/Modules/Modules_Furnished/Export

MP3_pipeline/Modules/Modules_Furnished/Other

MP3_pipeline/Modules/Modules_Furnished/Perfusion

MP3_pipeline/Modules/Modules_Furnished/Permeability

MP3_pipeline/Modules/Modules_Furnished/Relaxometry

MP3_pipeline/Modules/Modules_Furnished/SPM

MP3_pipeline/Modules/Modules_Furnished/Spatial

MP3_pipeline/PSOM

MRIFileManager

tools

tools/ClusterGMM_(StageClement)

tools/Color_bar_utilities

tools/DTI_version_1b

tools/Deconvolution

tools/FileHistory

tools/MICO_Algorithm

tools/MICO_Algorithm/MICO_3D

tools/Quality_Control

tools/Quality_Control/BIDS

tools/Quality_Control/BIDS/src/bids_tools_matlab

tools/Quality_Control/BIDS/src/bids_tools_matlab/External

tools/Quality_Control/BIDS/src/bids_tools_matlab/External/jsonlab-1.2

tools/Quality_Control/BIDS/src/bids_tools_matlab/External/jsonlab-1.2/examples

tools/Quality_Control/BIDS/src/bids_tools_matlab/External/sort_nat

tools/Quality_Control/BIDS/src/cfgFiles

tools/Quality_Control/BIDS/src/dicm2nii

tools/Quality_Control/Boutiques

tools/Quality_Control/Boutiques/src

tools/Quality_Control/Boutiques/src/External/GetFullPath_20161216

tools/Quality_Control/External/dicm2nii

tools/Quality_Control/html_report

tools/Quality_Control/html_report/External/knkutils

tools/Quality_Control/html_report/External/nansuite

tools/Quality_Control/imtool3D_td

tools/Quality_Control/imtool3D_td/External

tools/Quality_Control/imtool3D_td/External/interpmask

tools/Quality_Control/imtool3D_td/External/mask2poly

tools/Quality_Control/imtool3D_td/External/reduce_poly

tools/Quality_Control/imtool3D_td/src

tools/ROI_dyn

tools/Radiomics_metrics_mvallieres_TextureToolbox/Pre-processing

tools/Radiomics_metrics_mvallieres_TextureToolbox/Pre-processing/Normalization

tools/Radiomics_metrics_mvallieres_TextureToolbox/Pre-processing/Quantization

tools/Radiomics_metrics_mvallieres_TextureToolbox/Pre-processing/Wavelet

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/GLCM

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/GLRLM

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/GLRLM/Wei_Toolbox

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/GLSZM

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/Global

tools/Radiomics_metrics_mvallieres_TextureToolbox/Textures/NGTDM

tools/Radiomics_metrics_mvallieres_TextureToolbox/Utilities

tools/histnorm

tools/nansuite

tools/spm12

tools/spm12/@file_array

tools/spm12/@file_array/private

tools/spm12/@gifti

tools/spm12/@gifti/private

tools/spm12/@meeg

tools/spm12/@meeg/private

tools/spm12/@nifti

tools/spm12/@nifti/private

tools/spm12/@slover

tools/spm12/@slover/private

tools/spm12/@xmltree