2004/12/3
I've released a new version of aa and made it the default at the CBU. See the note below about tsdiffana if you're going to re-run an old analysis user script with this new version.
The new diagnostic jpegs make it easy to follow through how your automatic SPM analysis has gone. I hope this is useful! Rhodri
***aa beta 0.4: NEW FEATURES * added automatic saving of parameters sets and version number * added automatic saving of automatically identified series so that re-running is faster * added system for modifying CBU SPM defaults from within your user script with lines like aap.spm.defaults.normalise.write.vox=[3 3 3]; * improved error trapping for problems with pvconv.pl: now spots "not reconstructed" error and quits with a warning at this stage * added copying of .mat file during skull stripping * fixed problem so that if one subject is forcefully re-run (by deleting "done" flag) only this subject and not all the others will be run on subsequent stages * added new generation of diagnostic JPEG files as listed below. * added tsdiffana to processing pipeline Note that due to the addition of tsdiffana early in the pipeline, if you run an old aa_user script with the new version, it will rerun all stages after tsdiffana (e.g., most of the analysis). If you don't want this, either use the old version of aa by launching it with >> aa_ver0.3_beta or add the following line to your aa_user script: % list of tasks to perform (no tsdiffana) aap.tasklist.stages={'aamod_study_init','aamod_newsubj_init','aamod_copyfieldmaps', ... 'aamod_pvconv', 'aamod_copystructural','aamod_ana4dto3d', ... 'aamod_slicetiming','aamod_realign','aamod_undist','aamod_coreg', ... 'aamod_norm','aamod_undist_reslice'}; Thanks to Andy Lee for help with some of these features.
***DIAGNOSTIC JPEGS Name/ File directory/ Description diagnostic_aamod_ana4dto3d_rawmean Session raw mean as generated by ana4dto3d diagnostic_aamod_ana4dto3d_rawvar Session raw variance as generated by ana4dto3d diagnostic_aamod_tsdiffana Session output from tsdiffana diagnostic_aamod_realign Subject realignment display from SPM diagnostic_aamod_undist Subject evaluation of undistortion. Top pair of images are in distorted space and should be similar in shape and coregistered with each other. Left is distorted fieldmap magnitude, right is raw EPI. Bottom two images are in undistorted space and should be similar in shape and coregistered with each other, although not necessarily with the top two images. diagnostic_aamod_coreg Subject SPM output from coregistration of structural and undistorted EPI diagnostic_aamod_norm Subject SPM output from normalisation New in version beta 0.3
2004/11/9
PROBLEMS & FIXES (1) Problem in automatically identifying sessions in some datasets. This was due to an error message displayed by pvshow.pl. I've made the scripts handle these error messages more elegantly - you now get a warning but processing continues. If it can't find the sessions an error will still be generated. (2) The slice timing was set incorrectly in the default recipe, to 0.076 instead of 0.05. I'm sorry for this one - I've corrected it. This will effect rapid event-related designs in particular. Thanks to Andy Lee for spotting this.
aa is now used by http://www.cambridgeneuroimaging.com