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Getting Started with Image Analysis

Getting Started with Image Analysis

If you are reading this, you presumably can start VNC sessions, and connect a viewer, etc. If not, then see Getting Started With Linux.

You can get SPM-5 up and running by following the instructions at Getting Started SPM5.

Copying files from the WBIC

The WBIC uses a HSM system for storage. Please see the information about the WBIC network on their webpages [WWW] https://www.wbic.cam.ac.uk/ (these pages require a wbic account to access).

The current suggested way of copying a large number of files, which may be on tape, from the WBIC HSM is to copy directly (rather than by archiving/compressing). To copy your files, first touch_all.pl them to bring them off-tape, then copy them to the local storage by means of the scp command.

For example, if your user id is abc123, and your data is in a directory in your WBIC home directory called tobecopied

  • [WBIC cs1]$ touch_all.pl ~/tobecopied

to retreive those files from tape.

  • [BCNC]$ scp -rp gate1.wbic.cam.ac.ac.uk:~abc123/tobecopied/ /work/imaging1/abc123/copiedfromwbic/

to copy all these files to a directory in the /work/imaging1/ area. See the man pages on scp for more details.

Remember please copy large imaging files to one of the imaging filestores /work/imaging1-4 (*not* to your home directory, which should be used for small/office files only).

Once you have got your data over here, you'll need to convert your images and do Pre SPM Preprocessing. Have a look at Help with Imaging on each of the steps.

Note on WBIC structure

The "raw" data directories /pvCache etc are not mounted onto the gate0/gate1 machines. Thus to copy files from the raw data caches, you must log into a compute server (e.g. cs1) and copy the files into your home directory. Once in your home directory, the files will then be visible to the scp shell.

What If I Forget My VNC Password?

SSH on to one of the bcni servers and locate a directory called .vnc in your home directory (you will need to run ls -a to see hidden files & folders). In .vnc, you will be able to see a file called passwd, which unfortunately will be encrypted (too easy!) - but if you delete (rm) passwd and then run your VNC viewer, it will ask you for a new password. And no-one need ever know your embarrassment!

Alas Luke, your embarassment is public, and fated to increase... The 'correct' thing to do:

  1. Putty / ssh into iron (if outside the firewall)

  2. ssh to the machine running the desktop

  3. Stop your vnc desktops (no use if you have lost the password!) e.g.

    vncserver -kill bcni1:12 
  4. Delete the file ~/.vnc/passwd

  5. Run the vnc server to create a new desktop e.g.

    vncserver -depth 24 -geometry 1024x768 
  6. This command will ask you for your new password while running