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||surface||name of the surface file|| ||surface||name of the surface file. Egs: white or pial||
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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>||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>||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.||
MMTable
||<^#DDDDDD>'''Category'''||<^#DDDDDD>'''Flag'''||<^#DDDDDD> <'''Args'''> ||<^#DDDDDD>'''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:[[BR]]strncpy (annotation_fname, 'aparc.annot',[[BR]]sizeof(annotation_fname));[[BR]]load_annotation = TRUE;[[BR]]labl_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).[[BR]]Also: [[BR]]load_curv = TRUE;[[BR]]forcegraycurvatureflag = 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||

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

TkSurferGuide

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>

tksurfer (last edited 2011-06-27 12:05:43 by LouisVinke)