CONNECTING TO THE FILE SERVER
All data are stored on the file server, cbs. You can access from any lab computer.
1. In the menu on the top of your screen, select Go and then the last option in the drop-down menu: Connect to Server… (or use the hotkey Command+K).
2. In the server address box enter: smb://Storage.unr.edu/cbs and click connect
3. You are now connected to the server! Open a Finder window and you should find Storage.unr.edu under the SHARED heading on the left.
SETTING UP DIRECTORY STRUCTURE
Most of the scripts you will be using require a specific directory organization that is common to all experiments.
All MR data for the CLAB are stored on the file server in /Volumes/cbs/CLAB/MR_DATA
1. Create a folder for your experiment in the MR_DATA folder: /Volumes/cbs/CLAB/MR_DATA/my_new_expt (use a descriptive name for your experiment)
2. Within your experiment folder, create a new folder called scripts_default: /Volumes/cbs/CLAB/MR_DATA/my_new_expt/scripts_default
This is where we will be storing all the analysis scripts particular to your experiment. We will be copying these scripts from a set of general scripts that can be used by any experiment. You want to have your own copy instead of just using the general scripts for two reasons. First, you may need to make some changes that are particular to your experiment. Second, there may be updates over time to the general scripts. If you want to know exactly what analysis you ran, you want to have a record of the exact scripts you used. No one will change the scripts in your experiment folder.
3. Within your experiment folder, create new folders for every subject with their two-letter initial identifier: /Volumes/cbs/CLAB/MR_DATA/my_new_expt/FR
4. Scan in a .pdf of the scan plan for the experimental session for each subject, and place it in that subject's folder.
5. Download the raw data (.tgz file) for a subject, unzip it, and place the unzipped folders (there should be one pe4 run) in the subject's directory on the file server.
Note: it can be faster to unzip the rate data folder locally and then copy to the file server, rather than unzipping in the file server directory.
6. Within each subject folder, create a new folder called scripts: /Volumes/cbs/CLAB/MR_DATA/my_new_expt/FR/scripts
7. If plan on doing a GLM, download the stimulus times .1D data from your experiment and place them in a stim_times folder in the scripts directory for each subject: /Volumes/cbs/CLAB/MR_DATA/my_new_expt/FR/scripts/stim_times/cond1.1D
Now you're ready to start preprocessing!