Introduction/Overview

• This practice lesson focuses on data transfer with GLOBUS.

Install Globus

✅ Install Globus on your personal computer (if you haven't already).
 ● Windows Instructions
 ● Mac Instructions
 ● Linux Instructions

The Dataset

✅ Download the CAM003_bids_data.zip (226 MB) dataset from OSF to your computer.

The data was collected in Fall 2022 and is consistent with the ADNI4 protocol. It has been deidentified, converted to BIDS, and has the requisite IntendedFor fields for both fMRI and DWI processing. Scans of no interest have been removed, but they are enumerated in the included protocol (CAM.pdf). This dataset will be processed with suitable BIDS apps (e.g., mriqc, fmriprep, qsiprep, qsirecon) in subsequent lessons.

Globus Preferences

Globus Personal Connect runs in your status bar (Mac) or system tray (Windows). By default, only directories in your home area can be accessed.
✅ Check Preferences → Access to add Globus access to more directories.
Note: On Windows this is Options not Preferences
✅ Use the + (red box below, bottom) to add more directories, and make them writeable (Make sure you can access the directory where you placed the dataset).

Understand the Globus File Transfer Interface

Goal: Use Globus to transfer files between your computer and the HPC.
✅ As illustrated in the "Globus Transfer Demonstration" video, click the Globus icon and select  Web: Transfer Files:  .
This opens the File Manager window in your web browser with the File Manager icon selected (green box, below left). Two blank panels display in the file manager (like the one marked with the orange bar, below left). Each panel corresponds to an endpoint, but because no endpoint is defined, your panels are blank.

Panel 1 (right): The HPC

✅ Collection: Look at the collection box on the right (blue box). Select the endpoint you want in this panel:
✅ Type UA HPC Filesystems in the collection box search. This is a publically available endpoint so you should see UA HPC Filesystems among your search results. Select it, and authenticate if needed.
✅ Path 1: Below the collection box, type the directory path you want (purple box, below right). By default, your home directory is selected /~/. If your groups directory exists, you can type that in instead., e.g., /groups/dkp.
✅ Bookmark: To the right of each path box is a bookmark (red boxes). You can add a new bookmark for each endpoint and path. Once you choose a collection (computer), and a directory on that computer (path), you should click the bookmark icon. Try that now. (If a location is already bookmarked, then the bookmark is filled orange as shown below on the right).

Panel 2

✅ Click in the Collection box on the left (under the orange bar in the figure above).
As long as Globus Personal Connect is running, your personal computer should be listed under Your Collections (red box, below).
Computers marked in green are ready to connect. Any computer marked in red is inaccessible.
✅ Select your personal computer, and the path to the directory containing the dataset. Bookmark it.

Transfer the file

Following the example in the video (reproduced here from the previous lesson), select and transfer the CAM003_bids_data.zip dataset from your computer to the directory you have selected on the HPC.