Maxfilter Version 2.2
Look here for a brief [http://imaging.mrc-cbu.cam.ac.uk/meg/maxintro introduction and literature] about Maxfilter and its main feature, the Signal Space Separation method.
Example
Version 2.2. is currently the default when using the "maxfilter" command at the CBU.
This command will apply Maxfilter including Signal Space Separation (SSS), its temporal extension (ST), and movement compensation.
maxfilter -f input_file.fif -o output_file.fif -st -origin 0 0 45 -frame head -autobad on -movecomp -format short -force
For more information on these and other options, see the [attachment:Maxfilter_Manual2.2 Maxfilter 2.2 Manual].
Known problems and bugs
Maxfilter 2.2. cannot do downsampling and filtering at the same time as movement compensation. You will therefore have to run those in a separate step, e.g.
maxfilter -f input_file.fif -o output_file.fif -ds 4 -lpfilt 40
Diagnostics
You can get information about movement parameters using these [http://imaging.mrc-cbu.cam.ac.uk/meg/maxdiagnost scripts to analyse maxfilter output].
How to run Maxfilter at the CBSU
Via the CBU load balancing scripts
maxfilter - defaults to running version 2.2 on l43-l59
maxfilter-2.0 - runs version 2.0 on l24-l42
maxfilter-2.1 - runs v 2.1 on l43-l59
maxfilter-2.2 - runs v 2.2 on l43-l59
maxfilter_gui – runs using maxfilter-2.2 on l43-l59
To run without loadbalancing (i.e. on the current machine)
/neuro/bin/util/maxfilter – will run the default version of maxfilter for that machine (v2.0 on l24-42, v2.2 on l43-59)
The higher numbered machines also have the commands:
/neuro/bin/util/maxfilter-2.1
/neuro/bin/util/maxfilter-2.2
Running maxfilter this way does have the potential pitfall that the command /neuro/bin/util/maxfilter will run different versions depending on which machine you’re on.
By calling the actual binary files
/neuro/bin/util/<machine architecture>/maxfilter
/neuro/bin/util/<machine architecture>/maxfilter-2.1
/neuro/bin/util/<machine architecture>/maxfilter-2.2