MEG Analysis Code Changes

Hi, We have just pushed some core changes to the YNiC NAF Beamforming code. The change is that nafEpochRejection will no longer produce what have become known as "Epoch Rejection Files" but will instead produce "Slice Rejection Files". "Epoch Rejection File" are simply a list of epochs of data which should be rejected during analysis due to artifacts. This can be problematic, as if you change your pre-trigger or epoch duration, the timings of the epochs will move around and you will reject data you didn't mean to, whilst not rejecting the data around your artifacts. The replacement for these are "Slice Rejection Files". These are a list of slice ranges containing bad data - simply a list of comma separated slice ranges; one per line. The analysis (beamformer) code itself will continue to accept Epoch Rejection Files which are listed in YAML files for analysis, but will produce "Deprecation Warnings" to remind you that you should consider converting. If you wish to convert an existing Epoch Rejection File to a Slice Rejection File, you can do one of the following: * Use the nafEpochRejectToSliceReject tool (documented at /mnt/common/naf/naf-doc/userref/scripts/nafEpochRejectToSliceReject.html ) * Load the Epoch Rejection file into nafEpochRejection using the -e flag and it will output a slice rejection file. * Load you study into the Study Definer Tool (nafStudyDefiner) and it will offer to convert all epoch rejection files into slice rejection files and update the YAML file for you at the same time. Although the nafEpochRejection and nafStudyDefiner tool will still read Epoch Rejection Files (to perform conversions), they will no longer allow you to edit or output them; they will only work with and output slice rejection files. It should be noted that internally, all of the code now converts Epoch Rejection Files to Slice Rejection Files. This means that strictly speaking, if you have overlapping epochs, a single epoch number in an epoch rejection may now result in more than one epoch being rejected. This should be a rare corner case and if you want to fully understand and see what is going on, you can use the nafShowEpochs tool to list the epochs you have and, if a epoch or slice rejection file is present in your YAML file, whether or not they will be rejected. This is one of the final big changes before we make the NAF tools available by default on the system. More on that soon. Thanks, Mark -- Mark Hymers York Neuroimaging Centre