1. Installing SPM and Conn on Discovery - mind-lab-bos/MBI_Project_MRI_Analysis GitHub Wiki

** For the MCI project for the MIND Lab, Downloading SPM and Downloading Conn have already been done. If you will be processing fMRI data for the MCI project in the MIND Lab, skip to the add/savepath section. If you are starting your analysis on discovery for the first time, start by Downloading SPM and Conn to your discovery. **

Downloading SPM (Terminal on discovery)

  1. Open a terminal on discovery. Ensure you have navigated to the folder you would like to save SPM to and run the following two commands separately.

wget https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip

wget http://www.fil.ion.ucl.ac.uk/spm/download/spm12_updates/spm12_updates_r7771.zip

  1. Unzip each of the files using:

unzip spm12.zip

unzip -o spm12_updates_r7771.zip -d spm12

  1. Change permissions to ensure read, write, execute for all.

chmod -R 777 /work/mindlab/Matlab_Programs/spm12/ (chmod -R 777 /pathname/spm12/ if you have installed it somewhere else)

Downloading Conn Toolbox (Terminal on discovery)

  1. Open a terminal on discovery (or you can use the same one as you use for the SPM install). Ensure you have navigated to the folder you would like to save SPM to.

git clone https://github.com/alfnie/conn.git

  1. Change permissions to ensure read, write, execute for all.

chmod -R 777 /work/mindlab/Matlab_Programs/conn (chmod -R 777 /pathname/conn/ if you have installed it somewhere else)

Start here for MCI study analysis

Add/Save Path (Matlab on discovery)

  1. Open the Matlab interactive app on discovery. Add and Save spm12 path.

addpath /work/mindlab/Matlab_Programs/spm12

savepath()

  1. Add and Save conn path.

addpath /work/mindlab/Matlab_Programs/conn

savepath()