Getting to know xcp‐d derivatives

Getting to know xcp-d derivatives

Below are instructions to (1) download an R notebook that will walk through steps for plotting xcp-d derivatives, and (2) use AFNI to make a seed-to-voxel correlation map that we will explore with `fsleyes`.

Access FastX through the remote login:
https://fastx.divms.uiowa.edu:3443/

Step 1. Download R notebook that we'll run together in class:

• Open the terminal
• Change directories from your home directory to our xcp-d derivatives with the command: cd fmrilab/xcp_d_v0/
• Download R notebook by running this command in the terminal: wget -O functional-connectivity-lab_notebook.Rmd https://osf.io/q2uvj/download
• Click on this R notebook to open it

Step 2. Set up paths to AFNI:

• In terminal paste these lines in separate steps:

1. source /opt/AFNI/etc/AFNI_setup
2. /opt/AFNI/etc/AFNI_once_only > /dev/null

Step 3. Use AFNI to make a seed-to-voxel correlation map:

• Change directories to your seedFC folder: cd ~/fmrilab/xcp_d_v0/seedFC/

• Run this command to make a seed-voxel map with AFNI:

3dTcorr1D -prefix sub-004_LH-Vis-5_corrmap_zr.nii.gz -Fisher ../xcp_d/sub-004/func/sub-004_task-rest_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.nii.gz sub-004_seed_ts_LH_Vis_5.txt