This pipeline is a machine learning model based on a Logistic Regression to propose a binary diagnostic test (MS or non-MS) based on advanced MRI biomarkers (Central Vein Sign (CVS), Cortical Lesion (CL), Paramagnetic Rim Lesion(PRL)).
Enter the information about the subject, Run Analysis and get the diagnosis !
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Age: Enter the age of the subject in years as an integer or float (e.g. 45 or 45.3)
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CVS: Enter the results of the CVS assessment. Use one the following three rules:
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Total CVS: enter the % of CVS positive lesions across all eligible (*) brain lesions (e.g. 56%).
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Select6*: Enter the Select6* results for CVS.1 Either Yes or No
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Select3*: Enter the Select3* results for CVS.1 Either Yes or No
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If results from more than one CVS diagnostic assessments are entered together, only one will be used for inference, based on the following order: (1) Total CVS, (2) Select6*, (3) Select3*. Total CVS yields better diagnostic but is tedious and time consuming (manual counting of all eligible cerebral lesions).
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CL: Enter the number of CL of the subject.2
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PRL: Enter the number of PRL of the subject.3
(*) lesion eligibility for the CVS assessment following the NAIMS guidelines.4
Run Diagnosis
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Ontaneda, D., P. Sati, P. Raza, M. Kilbane, E. Gombos, E. Alvarez, C. Azevedo, et al. “Central Vein Sign: A Diagnostic Biomarker in Multiple Sclerosis (CAVS-MS) Study Protocol for a Prospective Multicenter Trial.” NeuroImage. Clinical 32 (2021): 102834. https://doi.org/10.1016/j.nicl.2021.102834.
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Filippi, Massimo, Paolo Preziosa, Brenda L Banwell, Frederik Barkhof, Olga Ciccarelli, Nicola De Stefano, Jeroen J G Geurts, et al. “Assessment of Lesions on Magnetic Resonance Imaging in Multiple Sclerosis: Practical Guidelines.” Brain 142, no. 7 (July 2019): 1858–75. https://doi.org/10.1093/brain/awz144.
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Absinta, Martina, Pascal Sati, Federica Masuzzo, Govind Nair, Varun Sethi, Hadar Kolb, Joan Ohayon, Tianxia Wu, Irene C. M. Cortese, and Daniel S. Reich. “Association of Chronic Active Multiple Sclerosis Lesions With Disability In Vivo.” JAMA Neurology 76, no. 12 (December 2019): 1474–83. https://doi.org/10.1001/jamaneurol.2019.2399.
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Sati, Pascal, Jiwon Oh, R. Todd Constable, Nikos Evangelou, Charles R. G. Guttmann, Roland G. Henry, Eric C. Klawiter, et al. “The Central Vein Sign and Its Clinical Evaluation for the Diagnosis of Multiple Sclerosis: A Consensus Statement from the North American Imaging in Multiple Sclerosis Cooperative.” Nature Reviews. Neurology 12, no. 12 (December 2016): 714–22. https://doi.org/10.1038/nrneurol.2016.166.
For windows OS, you can download the MSDT_setup.exe installation file from the install folder and execute it to easily install the program.
This tool can either be installed via the BMAT software or it can be downloaded and installed directly from this repository. For download and installation via BMAT, please refer to BMAT.
The procedure for the stand-alone download and installation is desribed hereunder. F
This software is written entirely in Python and thus requires Python to be installed to work properly. Pip is also needed to install the different packages that the software requires. Pip can sometimes be installed additionnaly when installing Python but not in every case, so it needs to be verified. The installation will be described for the different possible OS.
This link describes extensively how to install python on Linux.
The easiest solution to install Python is to use the Package Manager. For this, open a terminal and type the following command:
sudo apt-get install python
After the installation, you can verify that it all worked properly by typing:
python -V
This command should show you the version of Python.
Then, you can check if pip has been installed by typing:
pip -V
If the command show you the version of pip, it means that it has been installed. Otherwise, it will say that 'pip' is not recognized and needs to be installed. To install pip, you can type in the terminal:
sudo apt-get install python-pip
This will install pip, you can check that pip is well installed by checking its version.
The first possibility is to download Python via the microsoft store. This should download and install Python and Pip on your computer. To check if the installation has worked, you can open a command prompt or powershell and type:
python -V
to see the version of python and
pip -V
to see the verison of pip.
If there is no error, move on.
The second possibility is to download the installation package directly on the Python Website and install it via the classic installation process. Following this method, pip will not be installed with python. Here are the steps to install pip:
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Download the get-pip.py script to a folder on your computer.
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Open a command prompt in that folder or navigate to that folder.
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Run the script with the following command:
python get-pip.py
This should install pip. You can check if the installation worked by typing:
pip -V
Download the installation package directly from the Python Website and install it via the classic installation process. Following this method, pip will not be installed with python. Here are the steps to install pip:
-
Download the get-pip.py script to a folder on your computer.
-
Open a command prompt in that folder or navigate to that folder.
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Run the script with the following command:
python get-pip.py
This should install pip. You can check if the installation worked by typing:
pip -V
If it does not work, follow theses instructions on how to install pip.
This application can either be download via git, if you have git installed, via this command
git clone https://github.com/BMAT-Apps/MS_Diagnostic_Tool.git
Git is free and open source software for distributed version control: tracking changes in any set of files, usually used for coordinating work among programmers collaboratively developing source code during software development. Please refer to Git website for the intructions on how to install git on your specific OS
The second possibility is to download the source code in zip file directly from this webpage by clicking on Download Zip in the Code drop-down menu of this page (see Figure below). Then you can extract the zip file into your perferred directory.
To install all the required python package to run properly the application, open a terminal (**) in the MS-Diagnostic_Tool directory and run the following command:
pip install -r requirements.txt
(**)
To launch the application, open a terminal in the src folder of this repository and launch the file with this command:
python MS_diagnostic_tool.py