Differences between revisions 3 and 5 (spanning 2 versions)

Name

tksurfer - surfer 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

-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

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 3 as of 2004-08-06 13:41:22 → 
  Size: 1250
  Editor: DavidTuch
  Comment: Made into command page.
+   ← Revision 5 as of 2005-08-26 14:06:15 → ⇥
  Size: 2738
  Editor: KevinTeich
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-{{{
tksurfer - 1/2 sentence summary
}}}
+tksurfer - surfer visualizer
 Line 7:
-{{{
tksurfer [argA] -flag1 [arg2] -flag2 [arg3] [<options>]
}}}
-Line 11:
+Line 8:
-= Positional Arguments =
{{{
[argA]
  description
}}}
+{{{tksurfer [subject hemisphere surface] [options ...]}}}
-Line 18:
+Line 11:
-{{{
-flag1 [arg1]
  description
  description
-Line 23:
+Line 12:
--flag2 [arg2]
  description
  description
}}}
+||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}}}
-Line 29:
+Line 21:
-{{{
-flag3 [arg3]
  description
  description
-Line 34:
+Line 22:
--flag4 [arg4]
  description
  description
}}}

= Outputs =
{{{     
volume1 - description
volume2 - description
}}}
+||-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 46:
+Line 50:
-{{{
tksurfer foo -i f -o out
}}}
-Line 50:
+Line 51:
-= Example 2 =
{{{
tksurfer foo -i f -o out -f fvalue
}}}
+{{{tksurfer bert lh inflated}}}
-Line 56:
+Line 54:
-["othercommand1"], ["othercommand2"]
+TkSurferGuide
-Line 65:
+Line 64:
-description
-Line 67:
+Line 65:
-= 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 72:
+Line 68:
-Line 73:
+Line 70:
-= Methods Description =
## Suitable for cutting and pasting into publication.
## No WikiLinks should be used.
{{{
description
description
}}}

= Category =
## For example: CategoryFreeSurferCommandVolumeConversion
CategoryFreeSurferApplication