<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>maxoptions</title><revhistory><revision><revnumber>5</revnumber><date>2013-03-08 10:02:41</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>4</revnumber><date>2008-03-11 16:46:27</date><authorinitials>YuryShtyrov</authorinitials></revision><revision><revnumber>3</revnumber><date>2008-03-11 16:44:03</date><authorinitials>YuryShtyrov</authorinitials></revision><revision><revnumber>2</revnumber><date>2008-03-11 15:28:43</date><authorinitials>YuryShtyrov</authorinitials></revision><revision><revnumber>1</revnumber><date>2008-03-11 15:28:07</date><authorinitials>YuryShtyrov</authorinitials></revision></revhistory></articleinfo><section><title>Usage of MaxFitler from command line</title><para>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. </para><screen><![CDATA[usage: /opt/neuromag/bin/util/i686-pc-linux-gnu/maxfilter -f <infile> [options]
]]><![CDATA[
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
]]><![CDATA[
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)]]></screen></section></article>