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A simple command line tool and GUI for computing subtraction ictal SPECT coregistered to MRI (SISCOM). mnisiscom is exclusively intended for research use!

Project description

MNI SISCOM

MNI SISCOM is a Windows/Mac/Linux desktop and command line application for computing Subtraction ictal single-photon emission CT coregistered to MRI (SISCOM). The underlying Python library that implements the functionality of MNI SISCOM is also available on PyPi. Please cite the following paper if you use MNI SISCOM in a paper: [reference to come].

Screenshots

meningioma.app

Usage

Input MRI and SPECT volumes in NIfTI (.nii) format are supported. If you have raw DICOM images you can use a tool like dcm2nii (now available with MRIcroGL) to convert them to NIfTI format. Details about each parameter can be viewed by hovering over the label in the desktop app or via mnisiscom --help for the command line tool. Resulting images will be saved in the selected output folder.

Basic command line tool usage:

mnisiscom -t1 T1.nii -ii interictal_spect.nii -i ictal_spect.nii -o /path/to/output/folder

You can also launch the Desktop GUI from the command line: mnisiscom_gui

Installation

MNI SISCOM desktop app

Download MNI SISCOM: https://github.com/jeremymoreau/mnisiscom/releases

  • Windows: Double click mnisiscom_setup.exe and follow the instructions.
  • Mac: Double click mnisiscom.dmg and move mnisiscom.app to your Applications folder
    • If you get a notification that "mnisiscom" can't be opened because it is from an unidentified developer, right-click on the app and select Open, then click on the Open button.
  • Linux: Double click on mnisiscom.
    • If this doesn't work, you may need to right-click mnisiscom -> select Properties -> then the Permissions tab, and check the Allow executing file as program box.

Note 1: You must also install SPM12 standalone to use MNI SISCOM (SPM is used for SPECT/MRI image coregistration). See below for installation instructions for Windows, Mac, and Linux. Once installed, set the installation path of SPM in the settings menu of MNI SISCOM.

Note 2: Google Chrome or Chromium is also required to use the desktop app interface of MNI SISCOM.

MNI SISCOM command line tool & Python module

If you would like to use the command-line version of mnisiscom or the Python module, you can also install MNI SISCOM from PyPi. If you do not have python 3 yet, the Anaconda Python distribution is recommended: https://www.anaconda.com/distribution/#download-section

To install mnisiscom simply run: pip install mnisiscom

Note: On Windows you may need to install Visual Studio C++. See this question for more information: https://stackoverflow.com/questions/29846087/microsoft-visual-c-14-0-is-required-unable-to-find-vcvarsall-bat

SPM12 Installation

The standalone version of SPM12 is required for MNI SISCOM to run (it is used for SPECT and MRI image coregistration). For a more complete installation guide, see the SPM website: https://en.wikibooks.org/wiki/SPM/Standalone

Windows

  1. Download and install the Microsoft Visual C++ runtime components (vcredist_x64.exe) and the MATLAB Compiler Runtime (MCR) for SPM (MCRInstaller.exe) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/win64/

  2. Download the current version of SPM12 standalone (e.g. spm12_r7487.zip) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/

  3. Unzip the downloaded file and move the spm12 folder to where you would like to save it (e.g. in C:\Users\YourUsername\spm12)

  4. Start SPM12 to verify that it is properly installed (SPM12 will also need to unpack some files the first time it is run). Reboot your computer first if you run into any errors.

    • Open the spm12 folder (e.g. in C:\Users\YourUsername\spm12) and double click on spm12_win64.exe

Mac OS

  1. Download and install the MATLAB Compiler Runtime (MCR) for SPM (MCRInstaller.dmg) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/maci64/

  2. Download the current version of SPM12 standalone (e.g. spm12_r7487.zip) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/

  3. Unzip the downloaded file and move the spm12 folder to where you would like to save it (e.g. in /Users/YourUsername/spm12)

  4. Unzip the spm12_maci64.zip file in the spm12 folder

  5. Start SPM12 to verify that it is properly installed (SPM12 will also need to unpack some files the first time it is run). Reboot your computer first if you run into any errors.

    • In your Applications folder go to /Applications/Utilities and open the Terminal app
    • Type in cd /path/to/where/you/put/the/spm12/folder (e.g. cd /Users/YourUsername/spm12)
    • Then enter ./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/. Note: you may need to change /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ if you installed the MATLAB Compiler Runtime in a different location in step 1.

Linux

  1. Download and install the MATLAB Compiler Runtime (MCR) for SPM (MCRInstaller.bin) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnxa64/

  2. Download the current version of SPM12 standalone (e.g. spm12_r7487.zip) https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/

  3. Unzip the downloaded file and move the spm12 folder to where you would like to save it (e.g. in /home/YourUsername/spm12)

  4. Start SPM12 to verify that it is properly installed (SPM12 will also need to unpack some files the first time it is run). Reboot your computer first if you run into any errors.

    • Open a terminal
    • Type in cd /path/to/where/you/put/the/spm12/folder (e.g. cd /home/YourUsername/spm12)
    • Then enter ./run_spm12.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v713/. Note: you may need to change /usr/local/MATLAB/MATLAB_Compiler_Runtime/v713/ if you installed the MATLAB Compiler Runtime in a different location in step 1.

Note: If you have trouble installing SPM12 or the Matlab MCR for any reason, you can try downloading one of the more recent SPM12 standalone releases from here. In which case, you will need to download and install the matching Matlab MCR from the MathWorks website (e.g. if you download spm12_r7487_*_R2019b.zip, then download and install MCR version R2019b).

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