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{{{ tkmedit - 1/2 sentence summary }}} |
tkmedit - volume visualizer |
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{{{ tkmedit [argA] -flag1 [arg2] -flag2 [arg3] [<options>] }}} |
{{{tkmedit {[subject image_type]|[-f volume]} [surface] [options ...]}}} |
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= Positional Arguments = {{{ [argA] description }}} |
= Required Arguments = |
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= Required Flagged Arguments = {{{ -flag1 [arg1] description description |
TkMedit requires that a subject and image or volume be specified on the command line. |
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-flag2 [arg2] description description }}} |
||subject image_type||looks in $SUBJECTS_DIR/subject/mri for image_type|| ||volume||specify volume directory or file|| |
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{{{ -flag3 [arg3] description description |
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-flag4 [arg4] description description }}} |
||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|| ||-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)|| ||-headpts <points> [<trans>]||load head points file and optional transformation|| ||-interface script||scecify interface script (default is tkmedit.tcl)|| ||--version||print version of tkmedit|| |
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= Outputs = {{{ volume1 - description volume2 - description }}} |
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{{{ tkmedit foo -i f -o out }}} |
Load $SUBJECTS_DIR/bert/mri/T1 {{{tkmedit bert T1}}} {{{tkmedit -f $SUBJECTS_DIR/mri/T1/COR-.info}}} |
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{{{ tkmedit foo -i f -o out -f fvalue }}} |
Add a surface. {{{tkmedit bert T1 lh.inflated}}} = Example 2 = Load an overlay. {{{tkmedit bert T1 -overlay fsig.mgh -overlay-reg-file register.dat}}} |
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TkMeditGuide |
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| description | |
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= References = ## For example: ["Belliveau1991"] NameYear |
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. |
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= Methods Description = ## Suitable for cutting and pasting into publication. ## No WikiLinks should be used. {{{ description description }}} = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFreeSurferApplication |
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 |
-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) |
-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-file register.dat
See Also
Author
Links
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>