PetModelAutomation - MRC CBU Imaging Wiki

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Automating spm99 Analyses

SPM 99 PET analyses can be automated using the CBU CSV modfications to the standard SPM statistical design.

Download this file attachment:cbu_csv99_ui.m, put it somewhere in your Matlab run path, and run it from the Matlab command window:


for our version of spm 99b with local edits. This means that matlab will find my edited version of the file [ spm_spm_ui.m]. To install this feature outside the CBU, merely download the spm_spm_ui.m file from the link above, and save it into some directory on your matlab path that is in front of the SPM 99b distribution, and start SPM.The facility is a modified version of the SPM99b interface (spm_spm_ui.m) for specifying the design and image file locations in a PET study.

This automates the stages, after design type selection, of specifying group, subject, condition, replicate and covariate information by preparing a text file in advance and then telling SPM99b to read from this file. If you create a design in the standard point-click-type interface, a re-usable text file is created in the requisite format.

I have found this facility useful for running multiple 'what if' analyses - seeing what the effect is of dropping a subject, or a condition, or adding an extra covariate, etc. etc., at the cost of a few edits to a text file.

An equivalent version for the SPM99b interface (spm_spm_fmri_ui.m) for fMRI time series studies is under development.

With luck the planned upgrade to SPM99 will incorporate equivalent features. However, in the mean time, you may find this a useful time saving and accuracy enhancing addition.

Documentation is in

Let me know if you have any problems or comments.

[ Ian Nimmo-Smith] 12/10/99