Installation

BIDScoin can be installed and should work on Linux, MS Windows and on OS-X computers (this latter option has not been tested) that satisfy the system requirements:

  • dcm2niix
  • python 3.6 or higher

Dcm2niix installation

BIDScoin relies on dcm2niix to convert the source imaging data to nifti. Please download and install dcm2niix yourself according to the instructions. When done, make sure that the path to the dcm2niix binary / executable is set correctly in the BIDScoin Options in the [path_to_bidscoin]/heuristics/bidsmap_template.yaml file or in the Site specific / customized template file.

Python 3 installation

BIDScoin is a python package and therefore a python interpreter needs to be present on the system. On Linux this is usually already the case, but MS Windows users may need to install python themselves. See e.g. this python 3 distribution for instructions. They may also need to install the MS Visual C++ build tools (sorry for this pain).

BIDScoin installation

To install BIDScoin run the following command in your command-shell (institute users may want to activate a virtual / conda python environment first):

$ pip install bidscoin

This will give you the latest stable release of the software. To get the very latest (development) version of the software you can install the package directly from the github source code repository:

$ pip install git+https://github.com/Donders-Institute/bidscoin

If you want to edit the code or want to contribute back to the project, you can use the -e option:

$ pip install -e git+https://github.com/Donders-Institute/bidscoin#egg=bidscoin

If you do not have git (or any other version control system) installed you can download and unzip the code yourself in a directory named e.g. bidscoin and run (again, with or without the -e option):

$ pip install -e bidscoin

Updating BIDScoin

Run the pip command as before with the additional --upgrade option:

$ pip install --upgrade bidscoin

Caution

  • The bidsmaps are not garanteed to be compatible between different BIDScoin versions.
  • After a succesful BIDScoin installation or upgrade, it may be needed to (re)do any adjustments that were done on the Site specific / customized template file(s) (so make a back-up of these before you upgrade).