1. Command Line Options

1.1. 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

1.2. 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. i.e.

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.

1.3. Surface

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

tkmedit SUBJECT IMAGE_TYPE SURFACE

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

1.4. 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 i.e.:

tkmedit -overlay DATA_DIRECTORY/STEM -timecourse DATA_DIRECTORY/STEM

where STEM is the portion of the bfloat file data that comes before the _xxx slice number. i.e. the stem of a file set named minsig_000.bfloat through minsig_015.bfloat is minsig.

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

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, i.e:

tkmedit -overlay DATA_DIRECTORY/STEM -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/STEM

1.5. Segmentation

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

tkmedit -segmentation COR_DIRECTORY COLOR_FILE

The COR_DIRECTORY is the directory of the COR- files and the COLOR_FILE is the file to use as a color lookup table.

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

tkmedit -segmentation COR_DIRECTORY COLOR_FILE -segmentation-opacitty 0.6

1.6. 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