Installation

COMMIT is written in Python and requires Python 3; version 2 is no longer supported. Also, COMMIT internally makes use of several libraries, e.g.:

• AMICO for the generation/rotation of the response functions;
• DIPY to handle the diffusion data;
• NiBabel to read/write neuroimaging file formats;
• Cython to compile parts of the code.

The following installation procedures will install all these required libraries. In case of problems with a package, please refer to the corresponding website or write to us for assistance.

Install with PIP

Open the system shell and run:

pip install dmri-commit

This will download and install COMMIT from the Python Package Index.

PyPI available prebuilt wheels

	Windows	MacOS	Linux
Python 3.8	cp38-win_amd64 cp38-win32	cp38-macosx_x86_64 cp38-macosx_arm64	cp38-manylinux_x86_64 cp38-manylinux_aarch64
Python 3.9	cp39-win_amd64 cp39-win32	cp39-macosx_x86_64 cp39-macosx_arm64	cp39-manylinux_x86_64 cp39-manylinux_aarch64
Python 3.10	cp310-win_amd64 cp310-win32	cp310-macosx_x86_64 cp310-macosx_arm64	cp310-manylinux_x86_64 cp310-manylinux_aarch64
Python 3.11	cp311-win_amd64 cp311-win32	cp311-macosx_x86_64 cp311-macosx_arm64	cp311-manylinux_x86_64 cp311-manylinux_aarch64
Python 3.12	cp312-win_amd64 cp312-win32	cp312-macosx_x86_64 cp312-macosx_arm64	cp312-manylinux_x86_64 cp312-manylinux_aarch64

Note

MacOS wheels require MacOS 12.0 (Monterey) or later. If you are using an older version of MacOS, you can build dmri-commit from source (see the instructions below).

Install from sources

To be sure of having the latest updates, download the source code from this repository, open the system shell and go to the folder where you downloaded this repository, and run:

pip install . -U

Important

Windows requires the pthread-win32 static library to install the dmri-commit package. The library can be downloaded from https://github.com/GerHobbelt/pthread-win32. You need to compile the library as a static library and rename it to pthread.lib. Then, the PTHREAD_WIN_INCLUDE and PTHREAD_WIN_LIB environment variables must be set to the folder containing the header files and the library file, respectively.

Initial setup

COMMIT is now installed and can be imported in your Python interpreter as usual. The first time you use it, you need to run the following to configure it:

import commit
commit.setup()

Uninstall COMMIT

Open the system shell and run:

pip uninstall dmri-commit