= Usage of MaxFitler from command line =

GUI interface to maxfilter is limited, but can be helpful to discover the options the program has to offer. For the full power and scriptability, use the command line utility.

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usage: /opt/neuromag/bin/util/i686-pc-linux-gnu/maxfilter -f <infile> [options]

General options:
	-version               shows the version number of the program
	-help                  shows information of all options
	-v                     switches on verbose logging
	-f <infile.fif>        sets the name of the input file
	-o <outfile.fif>       sets the name of the output file
	-origin <x0 y0 z0>     sets the origin of the inside expansion
	                       (x0,y0,z0 must be in [mm])
	-frame <device/head>   sets the device/head coordinate frame
	-in <order_in>         sets the order of the inside expansion
	-out <order_out>       sets the order of the outside expansion
	-bad <chnos>           sets the list of static bad channels
	                       (logical chnos, e.g.: 0323 1042 2631)
	-autobad <on/off/n>    sets automated bad channel detection on or off
	                       n: scan from first n raw data tags (def n = 20)
	-badlimit <x>          threshold for bad channel detection (>ave+x*SD)
	-skip <intervals>      skips raw data sequences
	                       time intervals pairs in sec, e.g.: 0 30 120 150
	-format <short/long/float>
	                       stores the output in 16-bit short,
	                       32-bit integer or float format
	-force                 ignores program warnings
	-def                   shows default settings
	-maint                 shows the options needed for maintenance

MaxST options:
	-st [<buflen>]         applies the time-domain MaxST extension,
	                       optionally set data buffer length (def 4 sec)
	-corr <th>             set subspace correlation limit (def=0.98)
MaxMove options:
	-trans <fiff_file> | default
	                       transforms the data into the coil definitions
	                       of <fiff_file>, or into the default frame
	-movecomp [inter]      estimates and compensates head movements
	                       in continuous raw data
	                       (optionally for intermittent HPI)
	-headpos               estimates and stores head position parameters,
	                       but does not compensate movements
	-hp <posfile>          stores head position data in an ascii file
	-hpistep <n>           sets head position update interval in ms
	-hpisubt <amp/base/off> subtracts hpi signals: sine amplitudes,
	                       amp + baseline, or switch off (def = amp)
	-hpicons               check initial consistency isotrak vs hpifit
	-linefreq <f>          sets the basic line interference frequency
	                       (50 or 60 Hz)
	-lpfilt <corner>       applies low-pass IIR filtering
	                       (def corner = 120 Hz)
Other options:
	-site <name>           loads sss_cal_<name>.dat and ct_sparse_<name>.fif
	-cal <calfile> | off   uses the fine-calibration in <calfile>,
	                       or switch off
	-ctc <ctcfile> | off   uses the cross-talk matrix in <ctcfile>,
	                       or switch off
	-magbad                marks all magnetometers bad
	-regularize on/off     sets the component selection on or off
	-iterate [n]           uses iterative pseudo-inverse, n iteration loops
	                       default n=10; n=0 forces direct pseudo-inverse.
	-ds [f]                applies downsampling with low-pass FIR filtering
	                       f is optional downsampling factor (def = 2, max = 4)

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