Package: mnisiscom
MNI SISCOMMNI 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].ScreenshotsUsageInput 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 withMRIcroGL) to convert them to NIfTI format. Details about each parameter can be viewed by hovering over the label in the desktop app or viamnisiscom --helpfor 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/folderYou can also launch the Desktop GUI from the command line:mnisiscom_guiInstallationMNI SISCOM desktop appDownload MNI SISCOM:https://github.com/jeremymoreau/mnisiscom/releasesWindows: Double click mnisiscom_setup.exe and follow the instructions.Mac: Double click mnisiscom.dmg and move mnisiscom.app to your Applications folderIf you get a notification that"mnisiscom" can't be opened because it is from an unidentified developer, right-click on the app and selectOpen, then click on theOpenbutton.Linux: Double click on mnisiscom.If this doesn't work, you may need to right-click mnisiscom -> selectProperties-> then thePermissionstab, and check theAllow executing file as programbox.Note 1:Youmust also installSPM12standaloneto use MNI SISCOM (SPM is used for SPECT/MRI image coregistration). See below for installation instructions forWindows,Mac, andLinux. Once installed, set the installation path of SPM in the settings menu of MNI SISCOM.Note 2:Google Chromeor Chromium is also requiredto use the desktop app interface of MNI SISCOM.MNI SISCOM command line tool & Python moduleIf 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-sectionTo install mnisiscom simply run:pip install mnisiscomNote: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-batSPM12 InstallationThe standalone version ofSPM12is 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/StandaloneWindowsDownload 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/Note: If you are running an older (32 bit) version of Windows, download and install the files from this link instead:https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/win32/Download the current version of SPM12 standalone (e.g.spm12_r7487.zip)https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/Unzip the downloaded file and move thespm12folder to where you would like to save it (e.g. inC:\Users\YourUsername\spm12)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. inC:\Users\YourUsername\spm12) and double click onspm12_win64.exeMac OSDownload and install the MATLAB Compiler Runtime (MCR) for SPM (MCRInstaller.dmg)https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/maci64/Download the current version of SPM12 standalone (e.g.spm12_r7487.zip)https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/Unzip the downloaded file and move thespm12folder to where you would like to save it (e.g. in/Users/YourUsername/spm12)Unzip thespm12_maci64.zipfile in thespm12folderStart 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/Utilitiesand open the Terminal appType incd /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.LinuxDownload and install the MATLAB Compiler Runtime (MCR) for SPM (MCRInstaller.bin)https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnxa64/Note: If you are running a 32-bit Linux distro, download and install the file from this link instead:https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnx86/Download the current version of SPM12 standalone (e.g.spm12_r7487.zip)https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/Unzip the downloaded file and move thespm12folder to where you would like to save it (e.g. in/home/YourUsername/spm12)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 terminalType incd /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 fromhere. In which case, you will need to download and install the matching Matlab MCR from theMathWorks website(e.g. if you download spm12_r7487_*_R2019b.zip, then download and install MCR version R2019b).