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||-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.|| |
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{{{ tksurfer foo -i f -o out }}} |
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= Example 2 = {{{ tksurfer foo -i f -o out -f fvalue }}} |
{{{tksurfer bert lh inflated}}} |
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TkSurferGuide |
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| description | |
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= 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. |
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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
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
See Also
Author/s
Links
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>