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CBI Server Information
  • New user accounts use MUSC Single-Sign-On (i.e. NetID and MUSC password).

  • Many older users have likely never changed their passwords since originally issued by SCRA. If, and only if, your password is still MUSC4now!, please change it as soon as possible.
    • In a terminal window, type ‘ssh cairhive’ and login with your userid and password.
    • Then type ‘passwd’ and follow the prompts.
    • Logoff of cairhive. Passwords are synchronized across all the servers at the top of every hour. You may also need to change your VNC password. Use the vncpasswd command to do this.

  • A number of people have asked about or had concerns about data transfer from the 3T scanner to their respective upload directories on the server. A common reaction is to manually push the data from the scanner to CBI_PACS. When this happens, it makes it more difficult to isolate the cause of the problem. I’ve a setting on CBI_PACS in an attempt to correct this problem. If you are experiencing any data transfer problems, please let me know about it as soon as possible.

  • It is in everyone’s best interest to ensure that your studies have made it to the upload directories as soon as possible. I’ve recently discovered some issues that have existed since the server move in January. (read-only file system, bugs in the processing software) No data have been lost, but it’s easier to fix problems as soon as they’re noticed. All image data back to 2009 are currently in the PACS database. These data can be retrieved and pushed manually to the respective upload directories, but it takes time particularly when a problem, such as the one recently discovered, exists for an extended period of time.

  • 3T Workflow
    • As soon as scans are complete, they are transferred automatically to PACS.
    • Data also stay at the scanner console until Jeanette cleans up the storage to make room for more studies.
    • After arriving at the PACS, the IRB number from the study is matched to an IRB number in a configuration file. The IRB number is also used for accounting purposes.
    • If IRB number matches, the images are optionally converted to NIfTI, zipped together, and copied to the respective upload directory.
    • The processing software can send a confirmation email if transfer to the upload directory is unsuccessful. Important to check upload directories. It is safe to say that if you receive the email, at the very least, the data are on the PACS.

HowTo’s and FAQs

How do I change my server password?

If you are a “new” user (mid-2012 and after), and if your userid and password are your NetID and MUSC password, your server password will not change until you change your MUSC password. The servers are synchronized with the MUSC single sign-on system.

Many older users have likely never changed their passwords since originally issued by SCRA. If your password is still something like “MUSC4now!”, change it as soon as possible.

After logging in,

  • Type ‘ssh cairhive’ in a terminal window and login with your userid and password.
  • Type ‘passwd’ and follow the prompts.
  • Logoff cairhive. Passwords are synchronized across all the servers at the top of every hour. You may also need to change your VNC password. Use the vncpasswd command to do this.

How do I get an account on the CBI servers?

Contact Mark Van Horn at 6-2468 or vanhornm@musc.edu with the user’s name and NetID. A logon package will be sent as soon as the account is set up.

How do I set up a new study?

Send the following information to Mark Van Horn at vanhornm@musc.edu:

  1. IRB number (this is used for scheduling in calpendo and for post-processing of the scans.
  2. The study name.
  3. A contact email or addresses.
  4. A list of people that should have access to the data.

Where’s my data? I just did a scan and my data are not in the upload directory. Or some of my data are missing.

Data from the 3T scanner at 30 Bee St. transfer automatically to the CBI PACS (Picture Archiving and Communication System). After arriving at the PACS, The IRB number is used to search a configuration file. If a match is found, images associated with the study are collected, put in a zip file, and transferred to the user’s upload directory. If the IRB number is not found, the data remain in PACS, but are not sent to the upload directory. In some cases, images may be missing from the zip file. If the study does not arrive in the upload directory or if images are missing, contact Mark Van Horn at 6-2468 or vanhornm@musc.edu.

How can I transfer my data to my computer?

WinSCP (Windows Secure Copy or the Mac equivalent, Fugu) is distributed with the server logon package, and is probably the simplest way to transfer images between the PC and the server.

How do I convert my data format?

There are a wide variety of tools available to convert images from one format to another. While there are a multitude of image formats in use, the most common at MUSC are DICOM (Digital Imaging and Communications in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative). The de facto standard conversion software for DICOM-NIfTI conversion is dcm2nii (command-line) and dcm2niigui (GUI), both of which are available on the servers. They are also available for download (http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html). If you are interested in converting other image formats, contact Mark Van Horn at either vanhornm@musc.edu or 876-2468.

What are the server hostnames and IP addresses?

HostnameIP Address
hornet128.23.150.62
hivelogin128.23.150.181
compute-0-0 **

** To use compute-0-0, login to either hornet or hivelogin. Then type 'ssh -XY compute-0-0' to access compute-0-0 with a VNC session. Omit the -XY if a VNC session is not required.

 

68 President Street, MSC 120, Charleston, SC  29425
Phone: 843-876-2460  E-mail: cbi@musc.edu
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