Moving DICOMS to HPC

IF DATA IS ON XNAT

1. Connect to the FIU Network (FIU_SECUREWIFI) or via VPN if off campus
2. Navigate to the FIU XNAT Server
3. Log in using your credentials
4. Navigate to the page for the specific study you're working on.
5. Select the Subject from the list of subjects.
6. Select MR Session
7. Select Manage Files, then in the menu that pops up, uncheck all of the SNAPSHOTS
8. Select Download
9. After the Download has finished, extract the .zip archive
10. Copy the data to the HPC using a command of the following form scp -r extracted_directory_nameloginname@hpclogin02.fiu.edu:/home/data/madlab/dicoms/experimentname/subjectname/

This process may take some time

IF DATA IS ON A CD

1. Put CD containing DICOM files into the portable CD drive attached to computer.
2. Wait for CD drive to load.
3. Open a new terminal on your computer.
4. Navigate to /Volumes and then navigate to /CDROM on your computer
5. To copy all the files from the CD ROM to the correct folder on the HPC input

scp -r * loginname@hpclogin02.fiu.edu:/home/data/madlab/dicoms/experiment

FOR EXAMPLE: scp -r * amattfel@hpclogin02.fiu.edu:/home/data/madlab/dicoms/seqtrd/783126

The directory that you are secure copying (scp) on the cluster should exist. If you doesn't you'll need to ssh onto the cluster, navigate to the desired location using 'cd' and make the directory using 'mkdir'

FOR EXAMPLE:

1. ssh amattfel@hpclogin01.fiu.edu (after typing this in your terminal you'll be prompted to enter your password)...alternatively you can log on using a visualization node.
2. cd /home/data/madlab/dicoms/seqtrd
3. mkdir 783126

You will be prompted to enter your password. Note file transfer may take quite some time.