= 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