Running an analysis
From the Matlab command prompt, type the name of your User Script to run it. When aa starts, it runs several checks – warnings here give you advanced notice that your script may have problems at some later stage.
To restart an analysis, just type the User Script name again. The analysis will resume where it left off.
Change to the study directory and delete the “done_aamod_studyinit” flag. For example, to run an analysis from the very start for all subjects, type the following at a UNIX prompt:
cd /imaging/rhodri/mystudydir/aamod_autoidentifyseries rm done_aamod_autoidentifyseries
To track how far through the analysis it has got, the system writes small files in the form of “done_[module]”. Where a module has to be executed once per study, the “done_” file (also referred to as a “done_ flag”) will be in the study directory. Where a module needs to be executed once per subject, the done_ 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 done_ flags, then this stage and all stages following will be re-run.
Note that it isn’t always completely obvious whether a module is once-per-subject (e.g., realignment) or once-per-session (e.g., slice-timing), so it’s worthwhile checking in advance. For instance, to rerun the analysis for subject CBU0011 from the realignment stage and all stages following it, type the following at a UNIX prompt:
cd /imaging/rhodri.cusack/mystudydir/aamod_modulename/CBU0011 rm done_aamod_realign