Data Handling on CABI MR Systems

Contents

Siemens

The Siemens computer is a Sun running SunOS (a version of unix). Data is stored on one or more of three disks. After acquiring data you can either archive it to the optical drive or (more commonly) FTP it to another computer. You can FTP it to one of our unix workstations, or to our FTP site on claymore, or to a site outside of NKI.

Archiving data from the Siemens to an optical disk

  1. Put the optical disk in the optical drive.
  2. Right-click the mouse, then select file and then archive.
  3. To=OD and from=system (by default - you don't need to change them).
  4. Click Query and select your patient from the drop down list, then click Go.

Copying files from an optical disk to the Siemens

  1. Put the optical disk in the optical drive.
  2. Right-click the mouse, then select file and then copy.
  3. To=system and from=OD (by default - you don't need to change them).
  4. Click Query and select your patient from the drop down list, then click Go.

FTP-ing from the Siemens

Note: On the Siemens, data is stored on disk1, disk2, disk3, or a combination of them, which slightly complicates this process.

  1. Find and record the MR console-assigned ID
    1. Bring up an image of the subject on the console.
    2. Right-click mouse -> System -> Run -> Get Image File Name (check unique patient ID)
    3. Record:
      1. Patient ID # from SegPatient ID (must be 3-digit #, e.g. 222)
      2. File path: see whether the file is on disk1, disk2, or disk3
  2. Open Unix command window
    Hold Alt button and right-click mouse -> Programs -> command tool
  3. Change to directory that data is stored in
    cd /usr/appl/data/mrc/<disk>
    where <disk> is disk1, disk2, or disk3 (determined in step 1.C.ii)
  4. Check to make sure that the total number of images on <disk> is the correct number
    ls <ptID>* | wc -l
    -- <ptID> is the patient ID determined in step 1.C.i and wc is the unix word count program. The -l option means to count lines rather than words.
    Note: if the number of images on <disk> is not the correct number, the other images should be on one of the other disks. You can cd to another disk (step 3) and see if that has any of the images.
  5. Open an FTP connection to the computer to which you want to send the data
    ftp <host>
    where <host> is the name or IP address of the remote computer. E.g. ftp marvin or ftp claymore
    Transferring data to the CABI workstations (AFS). If you want to transfer data to your CABI unix account or temp space on AFS, you can FTP to a CABI unix workstation such as marvin or rimmer. (You can use any CABI unix workstation, since the data will end up on one of the AFS fileservers and be available on all of the workstations.) Use your unix (AFS) username and password.
    Transferring data to the CABI FTP server. If you want to make your data available outside NKI (for example if you collaborate with others outside NKI), you can put your data on claymore's FTP site at claymore.rfmh.org. Use the visitor username and password.
  6. Create a subdirectory on the remote computer to store the images that you will send.
    cd <directory>
    mkdir <subdirectory>
    where <directory> is the name of the directory on the remote computer in which you will create the subdirectory (for example, your last name) and <subdirectory> is the name of the subdirectory that you want to create. We often use the patient ID as the name of the subdirectory.
  7. Change to the subdirectory
    cd <subdirectory>
  8. Change FTP mode to binary, turn off prompts, and transfer files
    binary
    prompt
    mput <ptID>*     (e.g. mput 222*)
    Note: Sometimes you will get an error saying that there are too many files to FTP at once. In that case you will need to FTP the files in groups. E.g., do mput 222-1*, then when that is finished do mput 222-2*, etc.
    Note: If the images on the Siemens were on different disks, you can use the FTP command lcd to change the local directory. E.g., if you have just FTPed from disk3 but there are more files on disk2, you can use the command lcd /usr/appl/data/mrc/disk2 and then FTP files from disk2 to the remote computer.
  9. Check to confirm that all files have been transferred and exit the FTP program.
    ls <ptID>* (e.g. ls 222*)
    bye

The CABI unix workstations are ghana, kryten, lister, rimmer, trillian, sulcus, wonko, zaphod, and zarquon. (There are additional ones in people's offices.) You can ftp to any of them; however, sulcus (the oldest workstation) is slow and people often run MEDx (which can be resource intensive) on kryten.

Useful commands in ftp:

help   get help on ftp commands
cd   change directory on remote computer
lcd   change directory of local computer (Siemens)
pwd   print working directory (current directory) on remote computer
mkdir   create a new subdirectory on remote computer
prompt   prompting on/off (toggles)
binary   set to binary mode to transfer image files
ascii   set to ascii mode to transfer text files
put   send a single file to the remote computer
mput   send multiple files to the remote computer
get   get a single file from the remote computer
mget   get multiple files from the remote computer
dir   list files in current directory on remote computer

Backing up data to CD

After transferring data to a CABI unix computer, it is often desirable to make your own backup to CD. (Note that every night we back up users' home directories to our tape backup system, but not the dv* volumes (dv01, dv02, etc.) where users often store their data.) How to burn your data to CD in linux is described here. After burning the CD, we suggest that you double-check it (for example, try to read it on a PC) because some CDs fail.

SMIS

Both the 3T and 7T SMIS machines have a "console" PC and a "server" PC, each of which runs Windows NT. When the clinical software is used, data is automatically stored on the server. Otherwise, data is acquired on the console and should be moved to the server or to your PC (via Network Neighborhood) in order to free up disk space on the console. Once the data is on the server, it can be copied to a Jaz disk, FTP'd to our FTP site on claymore or to a site outside of NKI, or copied via the AFS client to our unix fileservers for processing on one of our unix workstations.

Jaz disks

Each SMIS server has a 2 GB Jaz drive which will write to 1 or 2 GB PC-formatted Jaz disks. Currently Jaz disks cost about $100 each, or you can buy a 3-pack (currently $240 from CompUSA). If you want to use a Jaz disk, insert it gently into the empty drive. If you encounter resistance, pull the disk out and realign it with the drive opening before reinserting. The drive is mounted as F: on our servers and has the label "Removable disk". You can copy data to it through Windows Explorer.

PC-formatted Jaz disks can be read on any of our linux computers which has a Jaz drive. You can back up data from Jaz disks onto CD's using xcdroast. Instructions for using Jaz drives and CD writers on linux are given below. Note that if you copy directly from Jaz disks to CD you can write on-the-fly (you don't have to master an image file first) since the data doesn't have to travel over the network.

How to use a Jaz disk in linux is described here.

FTP-ing from the SMIS servers

Data from the SMIS servers can also be transferred via FTP using the program FTP Voyager. It has a graphical interface and is largely self-explanatory. You can login to the FTP site on claymore or an FTP site outside of NKI. The interface has two panes, one representing the server and the other representing the remote computer (claymore or outside site). Otherwise it is similar to Windows Explorer. Files can be copied from one computer to another.

AFS client

How to use the AFS client in Windows is described here.

Backing up data to CD

After transferring data to a CABI unix computer, it is often desirable to make your own backup to CD. (Note that every night we back up users' home directories to our tape backup system, but not the dv* volumes (dv01, dv02, etc.) where users often store their data.) How to burn your data to CD in linux is described here. After burning the CD, we suggest that you double-check it (for example, try to read it on a PC) because some CDs fail.

This page was last updated on 12/5/2006.