Installation

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

  • dcm2niix
  • python 3.8 or higher
  • (FSL, optional and only needed when using the defacing tool to remove facial features from anatomical scans)

Dcm2niix installation

The default dcm2niix2bids plugin relies on dcm2niix to convert DICOM and PAR/REC files to nifti. To use this plugin, 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 Options section in your bidsmap or, for once and for all, put it in your Site specific / customized template bidsmap.

Python 3 installation

BIDScoin is a python package and therefore a python interpreter needs to be present on the system. On Linux and OS-X 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.

BIDScoin installation

To install BIDScoin on your system run the following command in a command-terminal (institute users may want to create and 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 --upgrade git+https://github.com/Donders-Institute/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:

$ pip install ./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)