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. Egs: white or pial |
These arguments are used to build a file name. The file will be:
$SUBJECTS_DIR/subject/hemisphere.surface
Optional Flagged Arguments
MMTable
Category |
Flag |
<Args> |
Description |
Input |
-curv |
|
Load ?h.curv |
Input |
-lrrev |
|
LeftRightRev = TRUE; |
Input |
-orig |
<orig_suffix> |
Use supplied orig suffix (default 'orig') |
Input |
-patch |
<patch_name> |
Load a patch file. |
Input |
-sdir |
<sdir> |
Subject dir (overrides SUBJECTS_DIR envt var) |
Input |
-sphere |
<sphere_reg_suffix> |
Uses supplied sphere suffix (default 'sphere') |
Input |
-white |
<white_suffix> |
Uses supplied white suffix (default 'white') |
Mask |
-mask |
<mrismaskfile> |
Load a mask file containing per-vertex values for a mask. Can be a list of per-vertex values stored in a volume-format file. (Is this feature supported? --GW) |
Mask |
-mask-thresh |
<mrismaskthresh> |
File of per-vertex values to which the per-vertex values in mrismaskfile are compared, resulting in each vertex being masked in or out. (...of what? Painting? Coloring? Stats? -- GW) |
Labels |
-annot or -annotation |
<annotation_fname> |
Imports an annotation file to provide s a set of labels on the surface. |
Labels |
-aparc |
|
Shortcut to load annotation aparc.annot:BRstrncpy (annotation_fname, 'aparc.annot',BRsizeof(annotation_fname));BRload_annotation = TRUE;BRlabl_draw_style = LABL_STYLE_OUTLINE; |
Labels |
-ctab or -colortable |
<colortable_fname> |
Load a default color table for labels and annotations. |
Labels |
-labels-under |
|
labels_before_overlay_flag = TRUE; |
Color |
-colscalebarflag |
<colscalebarflag> |
1 or 0. Turn on the color bar. |
Color |
-colscalebarvertflag |
<colscalebarvertflag> |
1 or 0. Display color scale bar |
Color |
-colscaletext |
<colscalebartextflag> |
1 or 0. Display text in color scale bar |
Color |
-gray |
|
Load ?h.curv and display it in grayscale. (As opposed to painting the surface plain gray, or portraying curv using red-green scale.) |
Color |
-scalebarflag |
<scalebarflag> |
1 or 0. Display the scale bar |
Display |
-delink |
|
Disables the feature where tool window 'docks' below surface-view window. |
Display |
-offset |
<offset> |
(float) 'Set the lighting offset value.' (Looks like it controls some aspect of brightness of surface. --GW) |
Display |
-title |
<tkstitle> |
Title for image window. |
Overlay |
-invphaseflag |
<invphaseflag> |
1 or 0. Invert the phase of the overlay data. |
Overlay |
-o or -ov or -overlay |
<functional_fname> |
Loads a file containing fMRI values. Could be either a volume file, or a file containing per-vertex functional data stored in a volume-format file (or possibly even a .w format file).BRAlso: BRload_curv = TRUE;BRforcegraycurvatureflag = TRUE; |
Overlay |
-orf or -ovreg or -overlay-reg |
<overlay_reg> |
Specify registration file for overlay. |
Overlay |
-overlay-reg-find |
|
Attempt to find a register.dat file in the same directory as the overlay data. |
Overlay |
-overlay-reg-identity |
|
Calculate an identity matrix for overlay registration. |
Overlay |
-ovnew |
|
UseNewOverlay=1 Invokes alternative coloring algorithm. (Not sure the purpose). |
Overlay |
-revphaseflag |
<revphaseflag> |
1 or 0. Reverse the phase of the overlay data. |
Overlay |
-truncphaseflag |
<truncphaseflag> |
1 or 0. Truncate the overlay data. |
Functional |
-fmid |
<fmid> |
(float) Set the functional midpoint value. |
Functional |
-foffset |
<foffset> |
(float) For functional, set the offset of the blue value. |
Functional |
-fslope |
<fslope> |
(float) Set the functional slope value. |
Functional |
-fthresh |
<fthresh> |
(float) Set the functional threshold value. |
Functional |
-t or -timecourse |
<timecourse_fname> |
Load a functional time course volume. |
Functional |
-timecourse-offset |
<timecourse_offset_fname> |
Loads the offset volume for the functional time course. |
Functional |
-timecourse-offset-reg-file |
<timecourse_reg> |
Specify a registration file for the time course offset. |
Functional |
-timecourse-offset-reg-find |
|
Attempt to find a register.dat file in the same directory as the time course offset data. |
Functional |
-timecourse-offset-reg-identity |
|
Calculate an identity matrix for time course offset registration. |
Functional |
-timecourse-reg-find |
|
timecourse_reg_type = FunD_tRegistration_Find; |
Functional |
-timecourse-reg-identity |
|
timecourse_reg_type = FunD_tRegistration_Identity; |
Functional |
-treg or -timecourse-reg |
<timecourse_reg> |
Also: timecourse_reg_type = FunD_tRegistration_File; |
Utility |
-h or -help |
|
Show Help info |
Utility |
-reassign |
|
Reassigns label vertex numbers (?) |
Utility |
-tcl |
<script_tcl> |
Load and run a tcl script |
Example 1
Load subject bert's lh.inflated surface.
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>