Thanks to Danny Mitchell, Rik Henson, Matt Davis & Adam Hampshire, who all contributed to this release.
You may download a PDF of a brief introduction given at the IIG on 5 June 2006 here: http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/iig_may2006_aanewfeatures.pdf
tsdiffana added to pipeline
Description: This was removed in the SPM5 aa ver 1. It has been added back in. tsdiffana time series variance tool run by default, output saved to "diagnostic_aamod_tsdiffana.jpg" Components: aamod_tsdiffana Authors: DM
normalisation using segment
Description: In SPM5, the "segment" tool can be used to normalise, and has been reported to work better. However, we found it to be unstable on our structural images, due an inhomogeneity in brightness across them, a probably result of spatial variations in sensitivity in the 12 channel coil we are using. So, this version implements a two pass process: a first pass to correct the inhomogeneity, and a second pass to do the normalisation. Components: aamod_norm_noss, aamod_norm_write Authors: RH, DM, RC
support for sparse imaging
Description: Interpolation across time in slice timing makes no sense with sparse imaging, where scans are far apart. This recipe has this stage removed. Components: minor changes to modules, new recipes Authors: MD
aa_report
Description: Produces an HTML summary of various diagnostic images. This tool is still under development. Components:aa_report Authors: RC
second level statistics
Description: This module trawls through your first level analyses and generates second level analyses of a one sample t-test for each first level contrast found. The contrast names and order must the same for all subjects or an error will be given. Components: aamod_model_secondlevel Authors: RC, RH
first level statistics
Description: This sets up a model for the single subject, first level event modelling. You will need to make a copy of this module to your aa directory and modify it to specify the particular design you ran. See the aa website for instructions on how to modify it. Components: aamod_model_firstlevel Authors: AH, RC
first level contrasts
Description: Runs contrasts on each subject at the first level. You will need to make a copy of this module to your aa directory and modify it to specify the particular design you ran. See the aa website for instructions on how to modify it. Components: aamod_contrasts Authors: AH, RC
modified shell calls so that it works in desktop
Description: When the Matlab Desktop is used with Matlab 6+7, an error is generated at the top of all shell calls (see http://www.mathworks.com/support/solutions/data/1-18DNL.html?solution=1-18DNL ). I've replaced all "unix" calls in the Matlab code with a call to a new wrapper script, aas_shell. This traps the error, taking off all lines that start with tcsh: from the top of the response. I did it this way to avoid the complication of having people change their .cshrc file. Components: aas_shell Authors: RC