PetModelAutomation - MRC CBU Imaging Wiki

Revision 3 as of 2006-09-05 11:29:31

Clear message
location: PetModelAutomation

Automating spm99 Analyses

SPM 99b PET analyses can be automated using my CSV edits to the standard SPM PET statistical analysis file.This facility has already been set up at the CBU. To use it, start spm 99b with the command line:

spm 99be

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