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> 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)