Dicom

To apply for a Dicom server account,

Send an email with the following information to the CCN Programmer Analyst Jonathan Hernandez.

1. Your Hoffman2 account ID if you have one.

2. CC your request to the PI whose group directory you need access to for approval.

Here are some ways to access the Dicom server.

SSH - Command Line

Mac/Linux/Unix

Simple SSH

Use the ssh command from a terminal:

ssh login_id@dicomservername

where login_id is replaced by your user account ID. The server host name will be sent by email when you receive your account. For CCN, it should be dcm.semel.ucla.edu. You will then need to enter your dicom server password.

After login, you will be under your home directory, /user/userid/

To access the group directory, use

cd /path/to/group_directory

(/path/to/group_directory should be sent to you together with your account information) For CCN, this will be /data/dicom/your_lab_folder_name

Windows

Use Putty for SSH terminal. See Hoffman's documentation for instructions on how to connect and set up functionality (such as running GUI applications).

Sharing File Systems with Mac

You can mount the Dicom file system to your local Mac computer using SSHFS

Please follow these similar instructions for Hoffman2

Usage:

sshfs -o idmap=user -o uid=1010 -o gid=20 userid@dicomserver:/path/to/groupdir ~/MOUNTPOINT

Copy files to Hoffman2

Please note that copying files off the Dicom server takes much longer when the scanner is in active use, due to the system prioritizing incoming data. As such, you may want to check the scanner calendar and wait for off hours or gaps in the schedule to do your download.

From SSH command line

After login to Hoffman2, run one of the following commands from one of the Hoffman2 server

scp -r dicomuserID@dicomserver:/path/to/group_directory/subject /path/to/your_directory/

or

rsync -av dicomuserID@dicomserver:/path/to/group_directory/subject /path/to/your_directory/

Script

setup_subject script is used to copy files from Dicom to Hoffman2, and do other processing such as nifti convert.