Diff for "ImagingComputingDevelopments" - MRC CBU Imaging Wiki
location: Diff for "ImagingComputingDevelopments"
Differences between revisions 20 and 21
Revision 20 as of 2008-02-10 18:15:45
Size: 3923
Comment:
Revision 21 as of 2008-02-14 03:25:19
Size: 4538
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
== 2008/02/14 Added VNC tools ==
I wrote a load balancing script for a glx enabled vncserver. The script balances only the vnc load. I chose to do it this way, because the vnc sessions will be very long term ~months, so balancing the cpu load is more or less irrelevant. If one of these glx vnc sessions is already open, a message will be sent to the user providing the port and machine that the active session is on. The script is called vncserver.glx and is located in /imaging/local/linux/bin/. I also added vncviewer, because it is way better than the default vncviewer on the RedHat install.

[DGW]

Developments to the imaging computing system

2008/02/14 Added VNC tools

I wrote a load balancing script for a glx enabled vncserver. The script balances only the vnc load. I chose to do it this way, because the vnc sessions will be very long term ~months, so balancing the cpu load is more or less irrelevant. If one of these glx vnc sessions is already open, a message will be sent to the user providing the port and machine that the active session is on. The script is called vncserver.glx and is located in /imaging/local/linux/bin/. I also added vncviewer, because it is way better than the default vncviewer on the RedHat install.

[DGW]

2008/02/07 Added function HeadMask.m to /imaging/local/spm/common_spm5andabove

This function attempts to mask out the vitamin E capsules from T1 weighted structurals. This is useful before producing a scalp mesh, which may otherwise be distorted. It may also improve normalisation to MNI space. It has been tested on seven subjects, never removing anything it shouldn't, and successfully removing the vitamin E capsules in six of the seven cases. (Including one patient with lesions; use at own risk.)

[DannyMitchell]

2008/02/06 Patched spm_getSPM manually

Fixed bug when saving design matrix from contrast manager as identified by Catherine Marie-Longtin, and solved by Ferath Kherif

put
cd(SPM.swd) at line 200,
just after the code : SPM.swd = swd; at line 199.

[RC]

2008/02/06 Added load balancing to FSL

All FSL 4.0.1 commands are now executed with load balancing.

Details... wrote python script /imaging/local/spm/loadshare/runfsl.py which launches an FSL command on the currently least busy machine. Then, /imaging/local/spm/loadshare/fslwrappers.py which makes symbolic links in /imaging/local/linux/bin/fsl-4.01/bin/loadshare/bin

This directory is now added by fsl_4.0.1_setup instead of the one with the actual commands in.

If you wish to run multiple scripts or jobs in parallel launch with separate xterms like this:

   xterm -e [your command 1] &
   xterm -e [your command 2] &

   e.g., xterm -e feat myscript.fsf &

[RC, MM]

2008/02/06 Delayed Software Documentation

Dan has been very naughty and not documented changes he made to the load balancing software. I updated (with Matthew Brett's help) several features of the software setup. We setup the Freesurfer and MNE scripts to source Freesurfer and MNE when they balance the load. We also setup so it will pass the SUBJECTS_DIR and SUBJECT variables. In order to ensure that the FSL version differences don't affect Freesurfer (which uses FSL), I have changed the way FSL works. FSL is no longer sourced by default. Each user who wants to use FSL needs to source FSL in each terminal window via the following scripts.

fsl_3.2_setup
fsl_4.0.1_setup

I'm sure there are some other details I have left out add questions here and I will fill out the replies.

[DGW]

2007/12/12 Added FSL 4.0.1

To use, type

fsl_4.0.1_setup

at the Linux prompt

2007/12/10 Tweaked load display

The load displayed when typing showload, or on launching SPM or MEG software was a bit verbose. I trimmed it. [RC]

2007/12/07 Updated MRIcro for Linux

Updated MRIcro to 1.39 build 4. Type startmricro & at Linux prompt to launch

[RC]

2007/12/05 Linux server OS version upgrade

Major upgrade. Linux servers l08-l21 upgraded to RedHat Enterprise Linux 4, and added to pool of machines used by default to run SPM 5 (under Matlab 7.3) and MEG.

Thanks very much to Rob Anthony for handling this so smoothly!

[RA]

2007/11/27 Updated load sharing back end, added load monitoring commands

New commands:

Type at Linux prompt

Description

showload

Shows load across all machines

bestmegmachine

Returns the machine currently loafing most

[RC]

2007/11/27 Control verbosity of output when starting spm or meg software

  • If you want the scripts to print less verbose output when you launch commands do
    • mkdir ~/.loadshare
    Then one of
    • touch ~/.loadshare/verbose_less
    or
    • touch ~/.loadshare/verbose_silent

[RC]

2007/11/27 MEG wrapper update

All previous Elekta commands and many new ones (e.g., maxave, maxfilter) are now called through a new wrapper. All arguments are passed straight along to the command, which will be launched on an appropriate machine. Start a new xterm to bring them into path. [RC]

CbuImaging: ImagingComputingDevelopments (last edited 2013-03-07 21:24:00 by localhost)