Diff for "SpmVersions" - MRC CBU Imaging Wiki
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spm {[versionnumber]} {nodesktop} {[machinename]} spm {[versionnumber]} {nodesktop} {fmri|pet} {[machinename]}
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where {} indicate a parameter is optional where {} indicate a parameter is optional and | indicates alternatives
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}}}

You'll probably usually want the FMRI defaults
{{{
spm fmri

Versions of SPM available at the CBU

Launch spm with

spm {[versionnumber]} {nodesktop} {fmri|pet} {[machinename]}

where {} indicate a parameter is optional and | indicates alternatives

By default Matlab is launched with a Java desktop tool. If you want to turn off the desktop add "nodesktop"

spm nodesktop

You'll probably usually want the FMRI defaults

spm fmri

See CbuComputingResources for information about which machines SPM runs on.

If you launch spm 99 or spm 2, it will run on machines l03-l07 under Matlab 6.5; if you use spm 5 it will run Matlab 7 on machines l03-l19. The machine with the lowest load (as measured every 15 mins) is chosen. If, however, you wish to run it on a specific machine use spm [machinename], e.g., spm l13

The versions of SPM available at the CBU are:

Initial setup for SPM startup scripts to work

The startup scripts will try and ssh into many machines to find the one with the lowest load. To do this without needing you to input anything, you need to have your ssh configuration set up to know about the various machines. In particular, you need add the identification numbers of the linux machines to your known_hosts file.

To add all the linux to your list of known hosts, type at the Linux prompt:

update_known_hosts

You should only need to do this once.

Versions in fairly current use

spm 5

The latest version of SPM, with all the current patches we could get. We recommend you use this version if you are starting a study from scratch, as it has some improvements over previous versions, particularly in spatial processing. It also has a number of extra features. Run SPM5 at the CBU, with:

spm

or

spm 5

at the unix prompt.

spm 2

Still widely used, and very similar to SPM5 in its basic functionality. To run SPM2 at the CBU:

spm 2

at the unix prompt.

spm 99

The oldest of the versions of SPM still in fairly common use, with all the patches we could get. We strongly recommend you switch to a new version, particularly for batch analyses, as the SPM99 batch system is very difficult to use. Run SPM99 at the CBU, with:

spm 99

at the unix prompt.

Want to see the code or install this tool where you are?

If you're at the CBU you may see the code, which is written in Python, in /imaging/local/spm/loadshare

If you're outside the CBU you may download the code from [http://www.mrc-cbu.cam.ac.uk/~rhodri/loadshare.tar here].

Other very old versions of SPM - for historical comparisons only

spm96 - original

SPM96 as originally distributed. We do not recommend you use this version of SPM, but instead use the patched version (see below).

spm96 - patched

This version is almost identical to the original version of spm96, but differs in that: 1. There have been some updates to fix little bugs. The bugs fixed are listed at the [http://www.fil.ion.ucl.ac.uk/spm/spm96.html the SPM web site 96 bug fix list]. The directory listing routine, spm_list_files, has been updated also, so that it does not crash when moving into automounted directories.

Our version includes the random effects toolkit. See the [http://www.fil.ion.ucl.ac.uk/spm/spm96.html SPM96 random effects toolkit] link for some explanation. Basically it enhances certain rarely used features of SPM96 to make random effects analyses easier. Follow the link above for some explanation of what a random effects analysis is. To get this patched version of SPM96 at the CBU, type:

spm 96

at the unix prompt.

spm 97

SPM97 is the patched version of SPM96 with the fMRI event related routines installed. Again, see the [http://www.fil.ion.ucl.ac.uk/spm/spm96.html SPM website 96 event related fMRI] link for details.To start SPM97 at the CBU, type:

spm 97

or

spm er

at the unix prompt.

spm 95

This is an older version of spm. There is little use for this for most people, but the code is useful for certain special occasions. In particular, it is much easier to see what the statistical analysis is doing in this version of the code.For SPM95, at the CBU, type:

spm 95

at the unix prompt.

CbuImaging: SpmVersions (last edited 2013-03-07 21:24:08 by localhost)