Creating a Miniconda Environment (for dcm to bids conversion) - mind-lab-bos/MBI_Project_MRI_Analysis GitHub Wiki

The following instructions are to be able to run the makebids_withfacenam_discovery.sh script. These steps only need to be completed once.

  1. Make sure you are in your home directory on Discovery. You can do that by clicking on "Change directory" on OpenOnDemand and type "/home/yourusername" before clicking on "Open in Terminal" or by typing the cd /home/<yourusername> command in Terminal.

  2. Install miniconda using these instructions. You should only need to follow steps 1-6 for now.

  3. Run the following commands in terminal one at a time (after completing step 2). This adds channels to conda.

conda config --add channels conda-forge

conda config --add channels defaults

conda config --add channels bioconda

  1. Create an environment to run the analysis.

conda create --name my_dcm2bids_env

conda activate my_dcm2bids_env (this should be run each time you want to run the tool)

  1. Install dcm2bids, dcm2niix, and numpy

conda install -c conda-forge dcm2bids

conda install -c conda-forge dcm2niix

conda install numpy