## see CommandTemplate and dtrecon as exmaples
= 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. Egs: white or pial||

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

{{{$SUBJECTS_DIR/subject/hemisphere.surface}}}

= Optional Flagged Arguments =

||<^#DDDDDD>'''Category'''||<^#DDDDDD>'''Flag'''||<^#DDDDDD> <'''Args'''> ||<^#DDDDDD>'''Description'''||
||<^>Input||<^>-curv||<^> ||<^>Load ?h.curv||
||<^>Input||<^>-lrrev||<^> ||<^>LeftRightRev = TRUE;||
||<^>Input||<^>-orig||<^> <orig_suffix> ||<^>Use supplied orig suffix (default 'orig')||
||<^>Input||<^>-patch||<^> <patch_name> ||<^>Load a patch file.||
||<^>Input||<^>-sdir||<^> <sdir> ||<^>Subject dir (overrides SUBJECTS_DIR envt var)||
||<^>Input||<^>-sphere||<^> <sphere_reg_suffix> ||<^>Uses supplied sphere suffix (default 'sphere')||
||<^>Input||<^>-white||<^> <white_suffix> ||<^>Uses supplied white suffix (default 'white')||
||<^>Mask||<^>-mask||<^> <mrismaskfile> ||<^>Load a mask file containing per-vertex values for a mask. Can be a list of per-vertex values stored in a volume-format file. (Is this feature supported? --GW)||
||<^>Mask||<^>-mask-thresh||<^> <mrismaskthresh> ||<^>File of per-vertex values to which the per-vertex values in mrismaskfile are compared, resulting in each vertex being masked in or out. (...of what? Painting? Coloring? Stats? -- GW)||
||<^>Labels||<^>-annot or -annotation||<^> <annotation_fname> ||<^>Imports an annotation file to provide s a set of labels on the surface.||
||<^>Labels||<^>-aparc||<^> ||<^>Shortcut to load annotation aparc.annot:<<BR>>strncpy (annotation_fname, 'aparc.annot',<<BR>>sizeof(annotation_fname));<<BR>>load_annotation = TRUE;<<BR>>labl_draw_style = LABL_STYLE_OUTLINE;||
||<^>Labels||<^>-ctab or -colortable||<^> <colortable_fname> ||<^>Load a default color table for labels and annotations.||
||<^>Labels||<^>-labels-under||<^> ||<^>labels_before_overlay_flag = TRUE;||
||<^>Color||<^>-colscalebarflag||<^> <colscalebarflag> ||<^>1 or 0. Turn on the color bar.||
||<^>Color||<^>-colscalebarvertflag||<^> <colscalebarvertflag> ||<^>1 or 0. Display color scale bar||
||<^>Color||<^>-colscaletext||<^> <colscalebartextflag> ||<^>1 or 0. Display text in color scale bar||
||<^>Color||<^>-gray||<^> ||<^>Load ?h.curv and display it in grayscale. (As opposed to painting the surface plain gray, or portraying curv using red-green scale.)||
||<^>Color||<^>-scalebarflag||<^> <scalebarflag> ||<^>1 or 0. Display the scale bar||
||<^>Display||<^>-delink||<^> ||<^>Disables the feature where tool window 'docks' below surface-view window. (2008-02-23: Flag accepted but feature broken. Will submit recommended changes --GW).||
||<^>Display||<^>-offset||<^> <offset> ||<^>(float) 'Set the lighting offset value.' (Looks like it controls some aspect of brightness of surface. --GW)||
||<^>Display||<^>-title||<^> <tkstitle> ||<^>Title for image window.||
||<^>Overlay||<^>-invphaseflag||<^> <invphaseflag> ||<^>1 or 0.  Invert the phase of the overlay data.||
||<^>Overlay||<^>-o or -ov or -overlay||<^> <functional_fname> ||<^>Loads a file containing fMRI values. Could be either a volume file, or a file containing per-vertex functional data stored in a volume-format file (or possibly even a .w format file).<<BR>>Also:     <<BR>>load_curv = TRUE;<<BR>>forcegraycurvatureflag = TRUE;||
||<^>Overlay||<^>-orf or -ovreg or -overlay-reg||<^> <overlay_reg> ||<^>Specify registration file for overlay.||
||<^>Overlay||<^>-overlay-reg-find||<^> ||<^>Attempt to find a register.dat file in the same directory as the overlay data.||
||<^>Overlay||<^>-overlay-reg-identity||<^> ||<^>Calculate an identity matrix for overlay registration.||
||<^>Overlay||<^>-ovnew||<^> ||<^>UseNewOverlay=1 Invokes alternative coloring algorithm. (Not sure the purpose).||
||<^>Overlay||<^>-revphaseflag||<^> <revphaseflag> ||<^>1 or 0. Reverse the phase of the overlay data.||
||<^>Overlay||<^>-truncphaseflag||<^> <truncphaseflag> ||<^>1 or 0. Truncate the overlay data.||
||<^>Functional||<^>-fmid||<^> <fmid> ||<^>(float) Set the functional midpoint value.||
||<^>Functional||<^>-foffset||<^> <foffset> ||<^>(float) For functional, set the offset of the blue value.||
||<^>Functional||<^>-fslope||<^> <fslope> ||<^>(float) Set the functional slope value.||
||<^>Functional||<^>-fthresh||<^> <fthresh> ||<^>(float) Set the functional threshold value.||
||<^>Functional||<^>-t or -timecourse||<^> <timecourse_fname> ||<^>Load a functional time course volume.||
||<^>Functional||<^>-timecourse-offset||<^> <timecourse_offset_fname> ||<^>Loads the offset volume for the functional time course.||
||<^>Functional||<^>-timecourse-offset-reg-file||<^> <timecourse_reg> ||<^>Specify a registration file for the time course offset.||
||<^>Functional||<^>-timecourse-offset-reg-find||<^> ||<^>Attempt to find a register.dat file in the same directory as the time course offset data.||
||<^>Functional||<^>-timecourse-offset-reg-identity||<^> ||<^>Calculate an identity matrix for time course offset registration.||
||<^>Functional||<^>-timecourse-reg-find||<^> ||<^>timecourse_reg_type = FunD_tRegistration_Find;||
||<^>Functional||<^>-timecourse-reg-identity||<^> ||<^>timecourse_reg_type = FunD_tRegistration_Identity;||
||<^>Functional||<^>-treg or -timecourse-reg||<^> <timecourse_reg> ||<^>Also: timecourse_reg_type = FunD_tRegistration_File;||
||<^>Utility||<^>-h or -help||<^> ||<^>Show Help info||
||<^>Utility||<^>-reassign||<^> ||<^>Reassigns label vertex numbers (?)||
||<^>Utility||<^>-tcl||<^> <script_tcl> ||<^>Load and 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>

If you are finding that the "Configure Overlay Display" dialog is being clipped, where it becomes impossible to see or interact with the buttons below a certain point, this has been found to happen with low-resolution monitors.  For an example, click [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurferclipped.jpg|here]] to see a screenshot (Thanks to Gonzalo Rojas Costa).  To fix this (only for FS v5.1.0), copy the file available [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurfer.tcl|here]] to your $FREESURFER_HOME/lib/tcl directory.  With this fix applied, the new dialog should look like [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurfernew.tiff|this]].