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Version 2.2. is currently the default when using the "maxfilter" command at the CBU. | Version 2.2. is currently the default on our 64-bit machines (see below for more details). |
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 on our 64-bit machines (see below for more details).
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