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>