Differences between revisions 4 and 8 (spanning 4 versions)

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

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>

-  ⇤ ← Revision 4 as of 2005-08-26 12:52:39 → 
  Size: 1160
  Editor: KevinTeich
  Comment:
+   ← Revision 8 as of 2006-01-19 17:31:28 → ⇥
  Size: 2954
  Editor: KevinTeich
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-tksurfer - surfer visualizer
+tksurfer - surface visualizer
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+||-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.||
-Line 24:
+Line 52:
-{{{
tksurfer foo -i f -o out
}}}
-Line 28:
+Line 53:
-= Example 2 =
{{{
tksurfer foo -i f -o out -f fvalue
}}}
+Load subject bert's {{{lh.inflated}}} surface.

{{{tksurfer bert lh inflated}}}
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+Line 58:
-["othercommand1"], ["othercommand2"]
+TkSurferGuide
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+Line 68:
-description
-Line 45:
+Line 69:
-= References =
## For example: ["Belliveau1991"]
NameYear
+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.
-Line 50:
+Line 72:
-Line 51:
+Line 74:
-= Methods Description =
## Suitable for cutting and pasting into publication.
## No WikiLinks should be used.
{{{
description
description
}}}

= Category =
## For example: CategoryFreeSurferCommandVolumeConversion
CategoryFreeSurferApplication