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| = Versions of SPM available at the CBU = | = Using various versions of SPM at the CBU = |
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| See CbuComputingResources for information about which machines SPM runs on. | Launch spm with |
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| Launch SPM with ''spm [versionnumber].'' By default, 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`. | {{{ spm {[versionnumber]} {matlab6.5 | matlab7.1 | matlab7.3} {nodesktop} {nojvm} {eeg|fmri|pet} {devel} {[machinename]} }}} where {} indicate a parameter is optional and | indicates alternatives |
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| The versions of SPM available at the CBU are: | You'll probably usually want the FMRI defaults {{{ spm fmri }}} |
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| == Versions in fairly current use == | By default, SPM 2 is launched under matlab 6.5, and SPM 5 under matlab 7.3 (upgraded from 7.1 14/8/2007). You may specify another version with the arguments matlab6.5, matlab7.1 and matlab7.3. See CbuComputingResources for information about which machines SPM runs on: this is dependent on the version of Matlab you are launching. The "devel" argument for spm 5 adds /imaging/local/spm/spm5/cbu_updates_devel to your path. This is the wild frontier of local imaging updates. 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 {{{ TIP: if you're using the default Matlab desktop, to break into a script while it is running, go to the white "launchspm_inner" window and press ctrl-C }}} If you have a directory in your homespace ~/matlab which contains the file .addtospm then ~/matlab will be added to the top of your SPM paths. == Other useful commands == || showload || Displays load on all machines || || bestmegmachine || Returns the machine currently loafing most || == Controlling the verbosity of output == 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 == Versions in current use == === spm 8 === 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. Run SPM5 at the CBU with: {{{ spm }}} or {{{ spm 8 }}} at the unix prompt. |
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| 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: | Still widely used, especially for people finishing up older studies. Run SPM5 at the CBU with: |
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| = 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 == |
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| Still widely used, and very similar to SPM5 in its basic functionality. To run SPM2 at the CBU: {{{ spm }}} or |
Not widely used. To run SPM2 at the CBU: |
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| 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: | Run SPM99 at the CBU with: |
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| = 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 |
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| 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 == |
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| SPM96 as orinally distributed. We do not recommend you use this version of SPM, but instead use the patched version (see below). | SPM96 as originally distributed. We do not recommend you use this version of SPM, but instead use the patched version (see below). |
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| 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. | 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. |
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| 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. | 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. |
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| 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: | 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: |
Using various versions of SPM at the CBU
Launch spm with
spm {[versionnumber]} {matlab6.5 | matlab7.1 | matlab7.3} {nodesktop} {nojvm} {eeg|fmri|pet} {devel} {[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
By default, SPM 2 is launched under matlab 6.5, and SPM 5 under matlab 7.3 (upgraded from 7.1 14/8/2007). You may specify another version with the arguments matlab6.5, matlab7.1 and matlab7.3. See CbuComputingResources for information about which machines SPM runs on: this is dependent on the version of Matlab you are launching.
The "devel" argument for spm 5 adds /imaging/local/spm/spm5/cbu_updates_devel to your path. This is the wild frontier of local imaging updates.
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
TIP: if you're using the default Matlab desktop, to break into a script while it is running, go to the white "launchspm_inner" window and press ctrl-C
If you have a directory in your homespace ~/matlab which contains the file .addtospm then ~/matlab will be added to the top of your SPM paths.
Other useful commands
showload |
Displays load on all machines |
bestmegmachine |
Returns the machine currently loafing most |
Controlling the verbosity of output
- If you want the scripts to print less verbose output when you launch commands do
- mkdir ~/.loadshare
- touch ~/.loadshare/verbose_less
- touch ~/.loadshare/verbose_silent
Versions in current use
spm 8
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. Run SPM5 at the CBU with:
spm
or
spm 8
at the unix prompt.
spm 5
Still widely used, especially for people finishing up older studies. Run SPM5 at the CBU with:
spm 5
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 here.
Other very old versions of SPM - for historical comparisons only
spm 2
Not widely used. To run SPM2 at the CBU:
spm 2
at the unix prompt.
spm 99
Run SPM99 at the CBU with:
spm 99
at the unix prompt.
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 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 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 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.