= 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.

{{{
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> ''sets subspace correlation limit (def=0.98) MaxMove

!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)
}}}