## see CommandTemplate and dtrecon as exmaples
= Name =

tkmedit - volume visualizer

= Synopsis =
{{{tkmedit {[subject image_type]|[-f volume]} [surface] [options ...]}}}

= Required Arguments =

TkMedit requires that a subject and image or volume be specified on the command line.

||subject image_type||looks in $SUBJECTS_DIR/subject/mri for image_type||
||volume||specify volume directory or file||

= Optional Flagged Arguments =

||surface||surface file to load (relative to $SUBJECTS_DIR/subject/surf or absolute)||
||-aux <volume>||load volume as auxilliary anatomical volume. relative to in $SUBJECTS_DIR/subject/mri or specify absolute path||
||-aux-surface <surface>||load surface as auxilliary surface. relative to in $SUBJECTS_DIR/subject/surf or specify absolute path||
||-main-transform <transform>||loads a display transform for the main volume||
||-aux-transform <transform>||loads a display transform for the aux volume||
||-bc-main <brightness> <contrast>||brightness and contrast for main volume||
||-mm-main <min> <max>||color scale min and max for main volume||
||-bc-aux <brightness> <contrast>||brightness and contrast for aux volume||
||-mm-aux <min> <max>||color scale min and max for aux volume||
||-conform||conform the main anatomical volume (dev version only)||
||-aux-conform||conform the aux anatomical volume (dev version only)||
||-overlay <file>||load functional overlay volume||
||-overlay-reg-find||find overlay registration volume in data dir||
||-overlay-reg-identity||generate identity for overlay registration volume||
||-overlay-reg <registration>||load registration file for overlay volume (default is register.dat in same path as volume)||
||-fthresh <value>||specify min, mid, and slope threshold||
||-fmid <value>||values for functional overlay display||
||-fslope <value>||(default is 0, 1.0, and 1.0)||
||-fsmooth <sigma>||smooth functional overlay after loading||
||-revphaseflag <1|0>||reverses phase display in overlay (default off)||
||-truncphaseflag <1|0>||truncates overlay values below 0 (default off)||
||-overlaycache <1|0>||uses overlay cache (default off)||
||-sdir <subjects dir>||(default is getenv(SUBJECTS_DIR)||
||-timecourse <file>||load functional timecourse volume||
||-timecourse-reg-find||find timecourse registration volume in data dir||
||-timecourse-reg-identity||generate identity for timecourse registration v olume||
||-timecourse-reg <registration>||load registration file for timecourse volume (default is register.dat in same path as volume)||
||-timecourse-offset <path/stem>||load timecourse offset volume||
||-segmentation <volume> <colors>||load segmentation volume and color file||
||-aux-segmentation <volume> <colors>||load aux segmentation volume and color file||
||-segmentation-opacity <opacity>||opacity of the segmentation overlay (default is 0.3)||
||-seg-conform||conform the main segmentation volume (dev version only)||
||-aux-seg-conform||conform the aux segmentation volume (dev version only)||
||-headpts <points> [<trans>]||load head points file and optional transformation||
||-interface script||scecify interface script (default is tkmedit.tcl)||
||--version||print version of tkmedit||


= Example 1 =

Load $SUBJECTS_DIR/bert/mri/T1

{{{tkmedit bert T1}}}
{{{tkmedit -f $SUBJECTS_DIR/mri/T1/COR-.info}}}

= Example 2 =

Add a surface.

{{{tkmedit bert T1 lh.inflated}}}
= Example 2 =

Load an overlay.

{{{tkmedit bert T1 -overlay fsig.mgh -overlay-reg register.dat}}}

= See Also =

TkMeditGuide

= Author =
KevinTeich

= Links =

FreeSurfer, TkMedit, TkSurfer

= Description =

TkMedit is the main volume viewer and editor for FreeSurfer. Use it to view volumes, overlay surfaces onto them in 2D, edit reconstruction defects, view functional overlays and time courses, view segmentations, and draw or edit labels.

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