Command Line Options

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

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 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-file or -timecourse-reg-file 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

TkMeditGuide/TkMeditReference/TkMeditCommandLineOptions (last edited 2008-04-29 11:45:10 by localhost)

-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-#pragma section-numbers on
-Line 7:
+Line 5:
-[[Navigation(children)]]



'''Index'''
-Line 12:
+Line 7:
-== Script ==
+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.
-Line 14:
+Line 9:
-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
-Line 22:
+Line 14:
+{{{
-Line 23:
+Line 16:
+}}}
-Line 24:
+Line 18:
-Where SUBJECT is a subject directory relative to the value of the SUBJECTS_DIR environment variable, and IMAGE_TYPE is a subdirectory of $SUBJECTS_DIR/SUBJECT/mri. i.e.
+Where {{{SUBJECT}}} is a subject directory relative to the value of the {{{SUBJECTS_DIR}}} environment variable, and {{{IMAGE_TYPE}}} is a subdirectory of {{{$SUBJECTS_DIR/SUBJECT/mri}}}. e.g.
-Line 26:
+Line 20:
+{{{
-Line 27:
+Line 22:
+}}}
-Line 28:
+Line 24:
-looks in $SUBJECTS_DIR/test_subject/mri/T1. If there is a COR- volume in this directory, or another kind of readable data, it will be loaded as the Main anatomical volume.
+looks in {{{$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.
-Line 30:
+Line 26:
-Another way to load anatomical data is with an explicit path or file name using the -f switch:
+Another way to load anatomical data is with an explicit path or file name using the {{{-f}}} switch:
-Line 32:
+Line 28:
-tkmedit -f PATH/TO/DATA/[FILENAME]
+{{{

tkmedit -f PATH/TO/DATA/FILENAME

}}}
-Line 36:
+Line 34:
-The Aux volume can be loaded with the -aux switch, i.e.
+The Aux volume can be loaded with the {{{-aux}}} switch, i.e.
-Line 38:
+Line 36:
+{{{
-Line 39:
+Line 38:
+}}}
 Line 40:
-This looks in $SUBJECTS_DIR/test_subject/mri/wm for a COR- volume.
+This looks in {{{$SUBJECTS_DIR/test_subject/mri/wm}}} for a COR- volume.
 Line 42:
-Note that TkMedit will not load without specifying a Main anatomical volume with the subject/image type method or the -f method.
+Note that TkMedit will not load without specifying a Main anatomical volume with the subject/image type method or the {{{-f}}} method.
 Line 49:
+{{{
-Line 50:
+Line 51:
+}}}
-Line 53:
+Line 55:
+{{{
-Line 54:
+Line 57:
+}}}
-Line 58:
+Line 62:
-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.:
+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 FILE}}} options, or their corresponding timecourse options, e.g.
-Line 60:
+Line 64:
-tkmedit -overlay DATA_DIRECTORY/STEM -timecourse DATA_DIRECTORY/STEM
+{{{

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

}}}
-Line 62:
+Line 68:
-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.
-Line 64:
+Line 70:
-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-file}}} or {{{-timecourse-reg-file}}} option with the registration file as the argument, e.g.:
-Line 66:
+Line 72:
-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/FILE -overlay-reg /PATH/TO/REGISTRATION_FILE.DAT

}}}
-Line 68:
+Line 76:
-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:
-Line 70:
+Line 78:
-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
+{{{

tkmedit -timecourse-offset DATA_DIRECTORY/FILE

}}}
-Line 77:
+Line 85:
-Use the -segmentation switch to load a COR- volume representing a segmentation. A color file is also necessary.
+Use the {{{-segmentation}}} switch to load a volume representing a segmentation. A color file is also necessary.
-Line 79:
+Line 87:
-tkmedit -segmentation COR_DIRECTORY COLOR_FILE
+{{{

tkmedit -segmentation VOLUME COLOR_FILE

}}}
-Line 81:
+Line 91:
-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:
-Line 83:
+Line 93:
-You can specify the opacity of the segmentation overlay with the -segmentation-opacity option:
+{{{
-Line 86:
+Line 95:
+}}}
-Line 90:
+Line 99:
-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.
+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.
-Line 92:
+Line 101:
+{{{
-Line 93:
+Line 103:
+}}}



== 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

}}}