Installation

Note

We strongly recommend using CuBIDS with environment management. For this, we recommend miniconda (miniforge for M1 Chip Mac Machines).

Once you’ve installed conda, initialize a new conda environment (for example, named cubids) as follows:

$ conda create -n cubids python=3.8
$ conda activate cubids

You are now ready to install CuBIDS. You can do so in one of two ways.

To obtain CuBIDS locally, we can use pip to download our software from the Python Package Manager (Pypi) by running the following commands:

$ pip install CuBIDS

Alternatively, you can clone the source code for CuBIDS from our GitHub repository using the following command:

$ git clone https://github.com/PennLINC/CuBIDS.git

Once you have a copy of the source, you can install it with:

$ cd CuBIDS
$ pip install -e .

We will now need to install some dependencies of CuBIDS. To do this, we first must install nodejs. We can accomplish this using the following command:

$ conda install nodejs

Now that we have npm installed, we can install the bids-validator using the following command:

$ npm install -g bids-validator@1.7.2

In our example walkthrough, we use bids-validator v1.7.2. using a different version of the validator may result in slightly different validation tsv printouts, but CuBIDS is compatible with all versions of the validator at or above v1.6.2.

We also recommend using CuBIDS with the optional DatLad version control capabilities. We use DataLad throughout our walkthrough of the CuBIDS Workflow on the Example Walkthrough page. To leverage the version control capabilities, you will need to install both DataLad and git-annex, the large file storage software DataLad runs under the hood. Installation instructions for DataLad and git-annex can be found here