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= Command Line Options =

<<TableOfContents>>

These are options that may be passed on the command line to load data and initialize settings. Note that an anatomical data must always be specified; tkmedit will not run without one. When examples are given of command line options, this is ommitted for clarity.


== Anatomical Volume ==

There are two ways to load anatomical data from the command line. The first is the default TkMedit mode for loading COR- volumes.

{{{
tkmedit SUBJECT IMAGE_TYPE
}}}

Where {{{SUBJECT}}} is a subject directory relative to the value of the {{{SUBJECTS_DIR}}} environment variable, and {{{IMAGE_TYPE}}} is a subdirectory of {{{$SUBJECTS_DIR/SUBJECT/mri}}}. e.g.

{{{
tkmedit test_subject T1
}}}

looks in {{{$SUBJECTS_DIR/test_subject/mri/T1}}}. If there is a COR- volume in this directory, or another kind of readable data, it will be loaded as the Main anatomical volume.

Another way to load anatomical data is with an explicit path or file name using the {{{-f}}} switch:

{{{
tkmedit -f PATH/TO/DATA/FILENAME
}}}

This method looks in the given directory or file for any recognizable data. It will be loaded as the Main volume.

The Aux volume can be loaded with the {{{-aux}}} switch, i.e.

{{{
tkmedit test_subject T1 -aux wm
}}}

This looks in {{{$SUBJECTS_DIR/test_subject/mri/wm}}} for a COR- volume.

Note that TkMedit will not load without specifying a Main anatomical volume with the subject/image type method or the {{{-f}}} method.


== Surface ==

To load a surface from the command line, add the name after the subject:

{{{
tkmedit SUBJECT IMAGE_TYPE SURFACE
}}}

or

{{{
tkmedit -f /path/to/volume/data SURFACE
}}}


== Functional Volume ==

Overlay data is loaded with the {{{-overlay}}} switch and time course data with the {{{-timecourse}}} option, with the concatenated path and stem as the argument. Additionally, a registration type must be specified with the {{{-overlay-reg-find}}}, {{{-overlay-reg-identity}}}, or {{{-overlay-reg FILE}}} options, or their corresponding timecourse options, e.g.

{{{
tkmedit -overlay DATA_DIRECTORY/FILE -overlay-reg-find -timecourse DATA_DIRECTORY/FILE -timecourse-reg-find
}}}

To enable functional registration, pass {{{-register}}} on the command line with no arguments.

{{{-overlay-reg-find}}} and {{{-timecourse-reg-find}}} look for a file called {{{register.dat}}} in the same directory as the data volume. {{{-overlay-reg-identity}}} and {{{-timecourse-reg-identity}}} generate an appropriate identity matrix using the anatomical and functional volume. To specify a registration file that is not in the same directory as the functional volume, use the {{{-overlay-reg}}} or {{{-timecourse-reg}}} option with the registration file as the argument, e.g.:

{{{
tkmedit -overlay DATA_DIRECTORY/FILE -overlay-reg /PATH/TO/REGISTRATION_FILE.DAT
}}}

To load an offset volume for the Time Course volume, specify it the same way as the Time Course volume but with the {{{-timecourse-offset}}} switch:

{{{
tkmedit -timecourse-offset DATA_DIRECTORY/FILE
}}}


== Segmentation ==

Use the {{{-segmentation}}} switch to load a volume representing a segmentation. A color file is also necessary.

{{{
tkmedit -segmentation VOLUME COLOR_FILE
}}}

You can specify the opacity of the segmentation overlay with the {{{-segmentation-opacity}}} option:

{{{
tkmedit -segmentation COR_DIRECTORY COLOR_FILE -segmentation-opacitty 0.6
}}}

== Head Points ==

Use the {{{-headpts switch}}} to load a head points file. This is a file of points indicating MEG/EEG sensor placement. A transform file is also required and can be specified on the command line.

{{{
tkmedit -headpts POINTS_FILE TRANSFORM_FILE
}}}

== Script ==

To automatically run a script, use the -tcl option, passing a script name. Tkmedit still requires anatomical data to be loaded before doing anything.

{{{
tkmedit -tcl SCRIPT_NAME
}}}