Getting ready to use AA
Once you’ve started a Matlab/SPM session, type
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>> aa_ver1 |
at the Matlab prompt to add the automatic analysis paths
Running an analysis
Once you’ve made your user script, just type its name to run it. When it starts to run, it does some checks, and so you may see some warnings. These give you advanced notice that your script may have problems at some stage
Restarting an analysis
To restart an analysis, just type the script name again. It will start from where it left off.
How do I force an analysis to start all over again?
Change to the study directory and delete the “done_aamod_studyinit” flag
Example
Type at UNIX prompt. When you run an analysis again it will redo the realignment stage and all stages after it for this subject.
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cd /imaging/rhodri/mystudydir |
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rm done_aamod_studyinit |
How do I force an analysis to start from a particular stage?
To track how far through the analysis it has got, the system writes small files that start with “done_...” and end with the module name. Where a module has to be executed once per study, the done_ file will be in the study directory. Where it has to be executed once per subject, it will be in the subject directory. Where it has to be done for every session, it will be in the individual session directories. If you delete one of these flags, then this stage and all others after it will be re-run. Note it isn’t always completely obvious whether a module is once-per-subject (e.g., realignment) or once-per-session (e.g., slice timing). See the Reference section 0 to check.
Example
Type at UNIX prompt. When you run an analysis again it will redo the realignment stage and all stages after it for this subject.
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cd /imaging/rhodri.cusack/mystudydir |
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cd CBU060500 |
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rm done_aamod_realign |