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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)

CbuMeg: maxoptions (last edited 2013-03-08 10:02:41 by localhost)