Name

tksurfer - surface visualizer

Synopsis

tksurfer [subject hemisphere surface] [options ...]

Required Flagged Arguments

subject

subject in which to look, inside $SUBJECTS_DIR

hemisphere

lh or rh

surface

name of the surface file

These arguments are used to build a file name. The file will be:

$SUBJECTS_DIR/subject/hemisphere.surface

Optional Flagged Arguments

-annotation <file>

Imports an annotation as a set of labels on the surface.

-colortable <file>

Loads the default color table for labels and annotations.

-overlay <file>

Loads a functional overlay volume.

-overlay-reg-file <file>

Specify the registration file for the overlay.

-overlay-reg-find

Attempt to find a register.dat file in the same directory as the overlay data.

-overlay-reg-identity

Calculate an identity matrix for overlay registration.

-fthresh <threshold>

Set the functional threshold value.

-fmid <mid>

Set the functional midpoint value.

-fslope <slope>

Set the functional slope value.

-foffset <offset>

Set the functional blue offset value.

-truncphaseflag <on>

Truncate the overlay data.

-revphaseflag <on>

Reverse the phase of the overlay data.

-invphaseflag <on>

Invert the phase of the overlay data.

-colscalebarflag <on>

Turn on the color bar.

-scalebarflag <on>

Turn on the scale bar.

-timecourse <file>

Loads a functional time course volume.

-timecourse-reg-file <file>

Specify the registration file for the time course.

-timecourse-reg-find

Attempt to find a register.dat file in the same directory as the time course data.

-timecourse-reg-identity

Calculate an identity matrix for time course registration.

-timecourse-offset <file>

Loads the offset volume for the functional time course.

-timecourse-offset-reg-file <file>

Specify the registration file for the time course offset.

-timecourse-offset-reg-find

Attempt to find a register.dat file in the same directory as the time course offset data.

-timecourse-offset-reg-identity

Calculate an identity matrix for time course offset registration.

-patch <file>

Load a patch file.

-offset <offset>

Set the lighting offset value.

-sdir <directory>

Use a different subjects directory.

-orig <suffix>

Specify the orig suffix

-tcl <script>

Run a tcl script.

Example 1

Load subject bert's lh.inflated surface.

tksurfer bert lh inflated

See Also

TkSurferGuide

Author/s

KevinTeich

Links

FreeSurfer, TkSurfer

Description

TkSurfer is the surface viewer for FreeSurfer. Use it to view surfaces in 3D and overlay data onto them, such as functional data, curvature, and field signs.

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>