PetModelAutomation5 - MRC CBU Imaging Wiki

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location: PetModelAutomation5

Automating SPM5 Analyses

SPM5 PET analyses can be automated using the CBU CSV modfications to the legacy SPM statistical design interface spm_spm_ui.m}} which is included in the {{{SPM5 distribution.

Download the file cbu_csv5_ui.m, put it somewhere in your Matlab run path, and run it from the Matlab command window:

>> cbu_csv5_ui

This utility is a modified version of the SPM5 legacy interface (spm_spm_ui.m) inherited from SPM99 and SPM2, for specifying the design and image file locations in a PET study.

The utility automates the specification of factors (group, subject, condition, replicate) and covariates, and selection of the image datasets, by preparing a text file in advance and then telling SPM99 to read from this file. Alternatively, you can use the utility to create a re-usable text file named design.csv in the requisite format if you use it create a design in the standard point-click-type interface.

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.

Documentation is in CbuCsv5Details.

Let me know if you have any problems or comments.

Updated by IanNimmoSmith on 5 September 2006.