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Scripting
Contents
This section assumes you are familiar with Tcl and how to write basic scripts.
Most of TkSurfer's functions have Tcl bindings. As you have probably noticed, the interface is just a Tk/Tix window. You can look at the interface script, tksurfer.tcl, to see how most of the functionality is used. Following is a list of Tcl commands defined by TkSurfer. You can use these commands in your own scripts and call them with the -tcl command line option to execute them on startup. TkSurfer can run in a kind of batch mode in this fashion, although it still requires X and has to be able to open its main window.
You can also enter these script commands from the shell that TkSurfer was launched in. You can use the Tcl source command to load a script file from the Tcl shell as well.
This list is provided for reference. If you can figure out something that works, great, but it is not officially a feature of TkSurfer.
Variables
These variables are used to turn on and off certain display characteristics. The way to set a flag is:
set gaLinkedVars(VARIABLENAME) VALUE SendLinkedVarGroup GROUP
Here is a table listing the variables, valid values, group names, and functionality.
Variable Name |
Valid Values |
Group |
GUI Location |
Description |
vertexset |
0-4 |
view |
View->Surface Configuration |
Use to set the current visible surface configuration. Use 0 for Main, 1 for Inflated, 2 for White, 3 for Pial, and 4 for Original. |
currentvaluefield |
0-8 |
view |
View->Overlay Layer |
Sets the current overlay layer. Should be followed with a call to SetOverlayField. |
labelstyle |
0-1 |
label |
View->Label Style |
Sets the label drawing style. Use 0 for filled and 1 for outline. |
redrawlockflag |
0,1 |
redrawlock |
View->Auto-redraw |
Sets the auto-redraw flag. |
curvflag |
0,1 |
view |
View->Curvature |
Controls curvature display. |
overlayflag |
0,1 |
view |
View->Overlay |
Controls overlay layer display. |
drawlabelflag |
0,1 |
label |
View->Labels |
Controls label display. |
labels_before_overlay_flag |
0,1 |
label |
View->Labels under Overlay |
Controls whether labels are drwn under the overlay. |
scalebarflag |
0,1 |
view |
View->Scale Bar |
Controls scale bar display. |
colscalebarflag |
0,1 |
view |
View->Color Scale Bar |
Controls the overlay color scale bar display. |
verticesflag |
0,1 |
view |
View->Wireframe Overlay |
Controls the wireframe display. |
drawcursorflag |
0,1 |
view |
View->Cursor |
Controls the cursor display. |
light0 |
0-1 (floating) |
scene |
View->Configure->Lighting |
Sets the first light value. |
light1 |
0-1 (floating) |
scene |
View->Configure->Lighting |
Sets the second light value. |
light2 |
0-1 (floating) |
scene |
View->Configure->Lighting |
Sets the third light value. |
light3 |
0-1 (floating) |
scene |
View->Configure->Lighting |
Sets the fourth light value. |
offset |
0-1 (floating) |
scene |
View->Configure->Lighting |
Sets the ambient light value. |
fthresh |
floating |
overlay |
View->Configure->Overlay |
Sets the overlay threshold minimum. |
fmid |
floating |
overlay |
View->Configure->Overlay |
Sets the overlay threshold midpoint. |
fslope |
floating |
overlay |
View->Configure->Overlay |
Sets the overlay threshold slope. |
falpha |
0-1 (floating) |
overlay |
View->Configure->Overlay |
Sets the overlay alpha value. |
ftimepoint |
integer |
overlay |
View->Configure->Overlay |
Sets the time point in the current overlay layer. |
fcondition |
integer |
overlay |
View->Configure->Overlay |
Sets the condition in the current overlay layer. |
colscale |
0-8 |
overlay |
View->Configure->Overlay |
Sets the overlay color scale type. Use 0 for Color Wheel, 1 for Heat, 4 for Two Cond G/R, 6 for Blue Red, 7 for Green Red, 8 for RYGB Wheel |
truncphaseflag |
0,1 |
overlay |
View->Configure->Overlay |
Sets the overlay Truncate flag. |
invphaseflag |
0,1 |
overlay |
View->Configure->Overlay |
Sets the overlay Inverse flag. |
complexvalflag |
0,1 |
overlay |
View->Configure->Overlay |
Sets the Complex flag. |
ignorezeroesinhistogramflag |
0,1 |
overlay |
View->Configure->Overlay |
Sets the Ignore Zeroes in Histogram flag |
cmid |
floating |
curvature |
View->Configure->Curvature |
Sets the midpoint value for the curvature display. |
forcegraycurvatureflag |
0,1 |
curvature |
View->Configure->Curvature |
Controls the binary gray curvature display. |
Commands
Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional.
align_sphere
- Given two marked points on the spherical surface, the first will specify the z-axis (the 1st pole of the sphere), and the second the x-axis (the orientation of the vertical meridian).
clear_all_vertex_marks
- Unmarks all vertices (necessary if the array of marked vertices and the vertex fields' marked status gets out of sync, e.g. you set marked fields directly).
clear_curvature
- Sets all curvature values to 0.
clear_ripflags
- Unrips all vertices.
clear_vertex_marks
- Unmarks the marked vertices.
close_marked_vertices
- Adds the first marked vertex to the end of the list of marked vertices.
compute_curvature
- Computes the curvature based on vertex positions.
curv_to_val
- Copies the curvature values into the first overlay values.
cut_line closed
Creates a line of ripped vertices on the surface between marked vertices in the order that they were marked. closed should be 0 for an open line, and 1 for a closed line.
cut_plane
- Cuts a plane based on four marked vertices: three to define the plane, and one to indicate which area to not cut.
dilate_ripped
- Dilates ripped areas, increasing their size by a vertex.
do_lighting_model light0 light1 light2 light3 offset
Changes the lighting setup for the scene. light0 through light3 are light levels from different positions and offset is overal ambient light. All values are floating points from 0-1.
draw_cursor vertexNumber on
Draws the specified vertex in blue if on, or in the background color if not on.
dump_vertex vertexNumber
Prints information about the specified vertex. vertexNumber is an integer.
f_to_t
- Squares and takes the absolute value for every overlay value field in the vertices.
find_orig_vertex_coordinates
Performs the Save Cursor function. Writes the current cursor location to the edit.dat file.
fix_nonzero_vals
- Sets the fixedval value for each vertex to 1 if the overlay value for that vertex is not 0, and to 0 if the value is 0.
flip_normals axes
Flips all the normal vectors at the vertices, changing the sign of the component values. axes is a string containing x, y, or z, or any combination, specifying which vector components to flip.
func_clear_selection
- Clears the functional time course selection.
func_graph_timecourse_selection
- Plots the graph for the time course. If more than one vertices are selected by the time course, will plot the average of the values.
func_load_timecourse fileName registrationType registrationFileName
Loads a time course from fileName. You must also specify a registrationType, which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the registrationType, use registrationFileName to specify the file. The time course will be displayed in a new window.
registrationFileName is necessary only of registrationType is file.
func_load_timecourse_offset fileName registrationType registrationFileName
Loads a time course offset from fileName. You should already have a time course loaded. You must also specify a registrationType, which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the registrationType, use registrationFileName to specify the file.
registrationFileName is necessary only of registrationType is file.
func_print_timecourse_selection fileName
- Prints a text file summarizing the data selected in the functional time course.
func_select_label
Selects the vertices in the current label for the functional time course. Needs a call to func_graph_timecourse_selection to plot the graph.
func_select_marked_vertices
Selects the marked vertices in the surface for the functional time course. Needs a call to func_graph_timecourse_selection to plot the graph.
invert_face faceNumber
Inverts the face normal at the numbered face. faceNumber is an integer.
fill_flood_from_cursor dontCrossPath dontCrossLabel dontFillUnlabeled dontCrossCuravature dontCrossThreshold multipleSeeds action argument
Initiates a flood fill starting at the cursor. dontCrossPath should be 1 or 0, specifying whether the fill should cross paths. dontCrossLabel should be 1 or 0, specifying whether the fill should cross into labels or only stay in unlabeled vertices. dontFillUnlabeled should be 1 or 0 and specifies whether the fill should fill unlabeled vertices. dontCrossCurvature should be 1 or 0, specifying whether the fill should fill vertices that have a different curvature sign than the first vertex. dontCrossThreshold should be 1 or 0, specifying whether vertices with overlay values below the functional threshold should be field. multipleSeeds should be 1 or 0, specfifying whether or not to use all marked vertices as new seeds. action should be one of the following:
0 |
No action, just mark filled vertices. argument is ignored. |
1 |
Make the filled vertices a new label. argument is ignored. |
2 |
Add the filled vertices to an existing label. argument should be the index of the label to add vertices to. |
3 |
Remove the filled vertices from an existing label. argument should be the index of the label to remove from. |
get_marked_vnos
- Returns a list of marked vertices.
get_selected_path_vnos
- Returns a list of vertices in the selected path.
invert_surface
- Inverts the vertex normals for all unripped vertices in the surface, but not the faces.
invert_vertex vertexNumber
Inverts the vertex normal at the numbered vertex. vertexNumber is an integer.
label_to_stat overlayField
Creates a new overlay layer with the values in the current label in overlay field overlayField.
labl_dilate label
Expands a label by adding all vertices immediately adjacent to the label. label should be a valid label index.
labl_erode label
Shrinks a label by excluding all border vertices in the label. label should be a valid label index.
labl_export_annotation fileName
- Exports all labels marked as structures to an annotation.
labl_import_annotation fileName
- Important an annotation file as a series of label.
labl_load fileName
Loads the label in fileName and adds it to the Labels window.
labl_load_color_table fileName
Loads a color table for labels to use from fileName.
labl_mark_vertices label
Marks the vertices in a label. label should be a valid label index.
labl_new_from_marked_vertices
- Creates a new label from the marked vertices.
labl_print_list
- Prints a list of label information to the shell
labl_print_table
- Prints the color table to the shell.
labl_remove label
Deletes a label. label should be a valid label index.
labl_remove_all
- Deletes all labels.
labl_save label fileName
Saves a label to fileName. label should be a valid label index.
labl_save_all prefix
- Saves all labels with a given prefix directory location.
labl_select label
Marks the vertices in a label. label should be a valid label index.
labl_select_label_by_vno vertexNumber
Selects a label containing the given vertex number. If there are multiple labels occupying this vertex, successive calls to this function with the same vertex number will cycle through those labels. vertexNumber should be a valid vertex index.
labl_set_color label red green blue
Sets the color for a label. label should be a valid label index. red, green, and blue should be integers from 0-255.
labl_set_info label name structureIndex visibility
Sets information for a label. label should be a valid label index. name is a text string that will show up in the Label window and in the label display. structureIndex should be -1 if it's a free label or a valid index in the current lookup table if it's a structure label. visibility should be 1 or 0.
labl_set_name_from_table label
Sets a label's name from its structure index from the lookup table. label should be a valid label index.
left_click x y
Simulates a click at the given window position. x and y should be integers.
make_lateral_view
- Changes the view to show the surface laterally.
mark_annotation vertexNumber
Will mark all vertices with the same annotation value as the annotation value at the specified vertex. vertexNumber is an integer.
mark_contiguous_vertices_over_thresh
Performs a flood fill from the cursor, marking all vertices that have overlay values above the threshold. (This is the Fill Stats tool.)
mark_contiguous_vertices_with_similar_curvature
Performs a flood fill from the cursor, marking all vertices that have curvature values the same sign as the curvature at the seed. (This is the Fill Curvature tool.)
mark_face faceNumber
Marks all vertices in the specified face. faceNumber is an integer.
mark_faces vertexNumber
Marks all vertices in the face to which the specified vertex belongs. vertexNumber is an integer.
mark_vertex vertexNumber on
Marks or unmarks a specified vertex. vertexNumber is an integer, and on is 0 for off and 1 for on.
mask_label labelFileName
- This reads and marks a label file, and then for every vertex not marked, clears the overlay values.
move_window x y
Moves the window to a new location. x and y are integers and are global screen coordinates, with 0,0 in the top left corner of the screen.
path_new_path_from_marked_vertices
- Creates a new path using the marked vertices. Connects the marked vertices in the order they were marked to create the path.
path_remove_selected_path
- Deletes the selected path.
path_select path
Selects the specified path. path should be a valid path index.
plot_curv closed
Draws a curve between marked vertices, and generates a summary file of all vertices on that curve, including values of all the overlay layers and the distance form the first point. closed should be 0 for an open curve, and 1 for a closed curve. The file is called surfer_curv.dat.
print_nearest_vertex_to_talairach_point x y z *
- Prints the nearest vertex to the specified talairach point x, y, z
only available in the internal dev version
read_annotations fileName
Deprecated, replaced by labl_import_annotation. fileName is an annotation file name, usually ending in .annot.
read_binary_curv
Loads a curvature file into the surface. Reads the file name from curv.
read_binary_decimation
Reads decimation values onto the surface from a file. Reads the file name from dec.
read_binary_dipoles
Reads dipole balues onto the surface from a file. Reads the file name from dip.
read_binary_patch
Reads a patch file into the surface. Will read the file name from patch.
read_binary_sulc
Reads a sulcus file into the curvature display. Reads the file name from sulc.
read_binary_surf
Loads the main surface from a surface file. Reads the file name from insurf.
read_binary_values
Deprecated, replaced by sclv_read_from_dotw. Will read the value file from val.
read_binary_values_frame
Deprecated, replaced by sclv_read_from_dotw_frame. Will read the value file from val.
read_canon_vertex_coordinates fileName
- Reads the vertex coordinates from a file into the canonical vertex set.
read_curv_to_val fileName
- Reads a curvature file into the first overlay layer.
read_fieldsign
Reads field sign values from a file. Will read the file name from fs.
read_fsmask
Reads the field sign mask from a file. Will read the file name from fm.
read_imag_vals fileName
Reads imaginary values from fileName.
read_labeled_vertices
Deprecated, replaced by labl_load. Will read the file name from label.
read_orig_vertex_coordinates
Reads the vertex coordinates from a file into the orig vertex set. Reads the file name from origcoords.
read_pial_vertex_coordinates
Reads the vertex coordinates from a file called ?h.pial where where ? is the current hemisphere into the pial vertex set.
read_really_matrix
Reads a matrix to transform the surface vertices. Reads the file name from subjtmpdir.
read_surface_vertex_set field fileName
Reads a set of vertices from the fle in fileName. field should be one of the following:
0 |
Main vertices |
1 |
Inflated vertices |
2 |
White vertices |
3 |
Pial vertices |
4 |
Orig vertices |
read_view_matrix
Reads a view matrix from a file. Reads the file name from subjtmpdir.
read_white_vertex_coordinates
Reads the vertex coordinates from a file called ?h.white where ? is the current hemisphere into the original vertex set.
really_center_brain
- Translates the surface coordinates to an average of all vertex coordinates.
really_rotate_brain_x degrees
Rotates the surface vertices around the x axis. degrees is a floating point number.
really_rotate_brain_y degrees
Rotates the surface vertices around the y axis. degrees is a floating point number.
really_rotate_brain_z degrees
Rotates the surface vertices around the z axis. degrees is a floating point number.
really_translate_brain rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
- Translates the surface vertices along the specified axes. All distances are in millimeters and can be floating point.
redraw
- Redraws the graphics window. It is necessary to call this after using other script commands to change the viewing state.
resend_to_subject
Calls send_to_subject with the sam subject name used in the previous send_to_subject call.
resize_brain
- Scales the brain according to the surface area to total area ratio.
resize_window size
Resizes the graphics window. size is an integer. The new window size will be sqaure with size x sizedimensions.
restore_ripflags mode
This will swap a set field vertex rip fields, and then rip the surface. If mode is 1, will swap the oripflag and ripflag fields. If mode is 2, will set the oripflag field from the ripflag field and the ripflag field from the origripflag field. After the rip, all vertices will be unmarked.
restore_initial_position
- Restores the view to a medial view.
restore_zero_position
- Restores the view to a medial view.
rip_all_vertices_except_contiguous_upripped
Performs a flood fill from the cursor, ripping all other vertices that are not contiguous to the seed point. (This is the Fill Uncut Area tool.)
rotate_brain_x degrees
Rotates the view around the x axis. degrees should be a floating point number.
rotate_brain_y degrees
Rotates the view around the y axis. degrees should be a floating point number.
rotate_brain_z degrees
Rotates the view around the z axis. degrees should be a floating point number.
save_rgb
Saves the contents of the view to a file in RGB format. Reads the file name from rgb.
save_rgb_cmp_frame
Reads the file name from rgb. Write an rgb frame file to be composed into a movie later.
save_tiff fileName
- Saves the current graphics contents as a TIFF file.
scale_brain zoomFactor
Zooms the view. zoomFactor is a floating point number; values greater than 1 make the brain appear larger, and from 0 to 1, smaller.
sclv_copy_all_view_settings_from_current_field
- Copies the settings from the current overlay to all other overlay layers.
sclv_copy_view_settings_from_current_field field
Copies the overlay settings from the current layer to another. field should be one of the field values in sclv_read_from_dotw.
sclv_copy_view_settings_from_field tofield toField
Copies the overlay settings from one layer to another. toField and fromField should be one of the field values in sclv_read_from_dotw.
sclv_get_normalized_color_for_value value
Converts an overlay value in the current field to an rgb color triple, returned as a list of floats. value should be a valid value in the current overlay layer.
sclv_load_label_value_file fileName field
Reads a label value file from fileName in an overlay field. field should be one of the field values in sclv_read_from_dotw. The label value file is a list of lines specifying a label name (such as an anatomical label from an LUT), a value, and a hemisphere.
sclv_read_bfile_values
Deprecated, replaced by sclv_read_from_volume.
sclv_read_binary_values
Deprecated, replaced by sclv_read_from_dotw.
sclv_read_binary_values_frame fileName field
Deprecated, replaced by sclv_read_from_dotw_frame.
sclv_read_from_dotw fileName field
Reads an overlay layer from the file specified in dotw format. field should be one of the following:
field |
Vertex field name |
Description |
0 |
val |
Overlay layer 0 |
1 |
val2 |
Overlay layer 1 |
2 |
valbak |
Overlay layer 2 |
3 |
val2bak |
Overlay layer 3 |
4 |
stat |
Overlay layer 4 |
5 |
imag_val |
Overlay layer 5 |
6 |
mean |
Overlay layer 6 |
7 |
mean_imag |
Overlay layer 7 |
8 |
std_error |
Overlay layer 8 |
sclv_read_from_volume field fileName registrationType [registrationFileName]
Reads an overlay layer from a volume file. The volume can either be a full 3D volume of overlay data, or a volume encoded value file. For the former, a registration file must be provided. field must be an overlay field, see sclv_read_from_dotw for values. registrationType should be one of the following:
0 |
Get registration from a file, and specify file in regitrationFileName |
1 |
Look for a file named register.dat in the same directory as the volume. |
2 |
Calculate an identity registration using the orig volume (must be present in subject's mri directory. |
If the registrationType is 0, then registrationFileName must be provided, otherwise it can be omitted.
sclv_send_histogram field
Tells tksurfer to resend the histogram information for a layer. Might be done after the overlay layer has changed, to force an update. field should be one of the field values in sclv_read_from_dotw.
sclv_send_current_field_info
Tells tksurfer to resend the overlay information for a layer. Might be done after the overlay layer has changed, to force an update. field should be one of the field values in sclv_read_from_dotw.
sclv_set_current_field field
Sets the current overlay field. field should be should be one of the field values in sclv_read_from_dotw.
sclv_set_current_threshold_from_percentile min mid max
Sets the current layer's threshold based on a percentile of values. min, mid, and max should be floating numbers from 0-1 representing percentages which will be mapped to overlay values to be used to set the threshold (for example: .92 .925 .99)
sclv_set_current_threshold_using_fdr rate markedOnly
Sets the current overlay's threshold using false discovery rate. rate is a floating point number representing the rate, and markedOnly should be 1 or 0 specifying whether to only calculate over marked vertices.
sclv_set_current_timepoint timePoint condition
Sets the time point and condition for the current overlay field. timePoint and condition should be integer values in the range of the current overlay's number of time pooints and conditions.
sclv_set_overlay_alpha alpha
Sets the overlay alpha. This controls the translucency for overlay display. alpha should be from 0 - 1, with 1 being opaque.
sclv_smooth numberOfSteps field
Smooths an overlay layer. numberOfSteps is an integer. field should be one of the field values in sclv_read_from_dotw.
sclv_write_dotw field
Writes the given overlay field to a dotw file. Reads the file name val. field should be one of the field values in sclv_read_from_dotw.
select_orig_vertex_coordinates
Performs the Read Cursor function. Reads the cursor location from the edit.dat file.
select_talairach_point x y z
Takes the given talairach coordinate, writes it to the edit.dat file, and then sets the cursor to that point. x y and z are floating point talairach values.
select_vertex_by_vno vertexNumber
Selects the given vertex as the cursor. vertexNumber is an integer.
send_current_labels
- Sends all the current information in the cursor and mouseover labels. Useful if you just set the cursor or if the vertex information under the cursor just changed, and want to force an update of the information.
send_spherical_point subjectName canonicalFileName origFileName
Converts the cursor to a cross-subject spherical point, then remaps it to a different subject's surface, and writes it to their edit.dat cursor file, so that subject use the Read Cursor command to get this cursor. subjectName is the subject for whom to write the cursor fiel. canonicalFileName is the file from which to read the canonical vetex positions. origFileName is the file from which to read the original vetex positions. Those filenames are relative to the subjectName.
send_to_subject subjectName
Calls send_spheric
curv_to_val al_point
set_current_vertex_set field
Sets the current vertex set (the one being displayed) to the named field. field should be one of the values in read_surface_vertex_set.
show_flat_regions surfaceFileName threshold
Reads vertex positions from surfaceFileName. For every vertex normal with a component longer than threshold, will set the overlay value at that vertex to the value of that component, otherwise sets the value to 0. threshold is a floating point number.
show_surf vertexSet
Moves the specified vertex set into the main vertex set position. vertexSet is white, pial, or inflate.
shrink numberOfSteps
Inflates the surface by the number of steps given. numberOfSteps should be an integer.
smooth_curv numberOfSteps
Smooths the curvature values by numberOfSteps, an integer
stat_to_val
- Copies the values of the stat field to the overlay value field.
swap_vertex_fields field field
A more general way of swaping vertex fields. field should be one of the following:
field |
Vertex field name |
Description |
0 |
curv |
Curvature display |
1 |
curvbak |
Backup curvature (not displayed |
2 |
val |
Overlay layer 0 |
3 |
imag_val |
Overlay layer 5 |
4 |
val2 |
Overlay layer 1 |
5 |
valbak |
Overlay layer 2 |
6 |
val2bak |
Overlay layer 3 |
7 |
stat |
Overlay layer 4 |
transform_brain
- Recenters the brain.
translate_brain_x distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
translate_brain_y distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
translate_brain_z distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
undo_last_action
- Undoes the last action.
val_to_curv
- Copies the first overlay values into the curvature values.
val_to_mark
- Will mark all vertices with overlay values greater than the overlay threshold.
val_to_stat
- Copies the values of the overlay value field to the stat field.
write_binary_curv
Saves the curvature values to a new file. Will read the file name from curv.
write_binary_dipoles
Write the dipoles to a file. Will read the file name from dip.
write_binary_patch
Saves the current surface as a patch. Will read the file name from patch.
write_binary_sulc
Saves the sulcus values (if loaded in the curvature set) to a new file. Will read the file name from sulc.
write_binary_surface
Saves the surface to a new file. Will read the file name from outsurf.
write_fieldsign
Saves the field sign values to a new file. Will read the file name from fs.
write_fsmask
Saves the field sign mask to a new file. Will read the file name from fm.
write_labeled_vertices
Saves all marked values to a label file. Will fill in the stat value of the file with the current overlay field's value. Will read the file name from label.
write_really_matrix
Writes the matrix used to transform the surface vertices. Reads the file name from subjtmpdir.
write_view_matrix
Write the current view matrix to a file. Reads the file name from subjtmpdir.
write_vrml mode
Writes a VRML version of the surface. Will read the file name from vrmlsurf. mode is 0 for pts, 1 for gray, and 2 for curv.
Index
Viewing Operations
align_sphere do_lighting_model draw_cursor left_click make_lateral_view move_window redraw rotate_brain_x rotate_brain_y rotate_brain_z scale_brain send_current_labels show_flat_regions translate_brain_x translate_brain_y translate_brain_z read_really_matrix read_view_matrix really_center_brain really_rotate_brain_x really_rotate_brain_y really_rotate_brain_z really_scale_brain really_translate_brain resize_brain resize_window restore_zero_position restore_initial_position transform_brain write_view_matrix write_really_matrix
I/O
func_load_timecourse func_load_timecourse_offset labl_export_annotation labl_import_annotation labl_load labl_load_color_table labl_save labl_save_all read_annotations read_binary_curv read_binary_decimation read_binary_dipoles read_binary_sulc read_binary_surf read_binary_values read_binary_values_frame read_binary_patch read_canon_vertex_coordinates read_curv_to_val read_fieldsign read_fsmask read_imag_vals read_labeled_vertices read_orig_vertex_coordinates read_pial_vertex_coordinates read_surface_vertex_set read_white_vertex_coordinates sclv_load_label_value_file sclv_read_bfile_values sclv_read_binary_values sclv_read_binary_values_frame sclv_read_from_dotw sclv_read_from_volume sclv_write_dotw write_binary_curv write_binary_dipoles write_binary_patch write_binary_surface write_binary_sulc write_fieldsign write_fsmask write_labeled_vertices write_vrml
Curvature Operations
clear_curvature compute_curvature curv_to_val fill_flood_from_cursor mark_contiguous_vertices_with_similar_curvature smooth_curv val_to_curv
Overlay Operations
curv_to_val f_to_t fill_flood_from_cursor label_to_stat mark_contiguous_vertices_over_thresh sclv_copy_all_view_settings_from_current_field sclv_copy_view_settings_from_current_field sclv_copy_view_settings_from_field sclv_get_normalized_color_for_value sclv_load_label_value_file sclv_read_bfile_values sclv_read_binary_values sclv_read_binary_values_frame sclv_read_from_dotw sclv_read_from_volume sclv_send_current_field_info sclv_send_histogram sclv_set_current_field sclv_set_current_threshold_from_percentile sclv_set_current_threshold_using_fdr sclv_set_current_timepoint sclv_set_overlay_alpha sclv_smooth sclv_write_dotw stat_to_val swap_val_val2 val_to_curv val_to_stat
Vertex Operations
fill_flood_from_cursor find_orig_vertex_coordinates fix_nonzero_vals flip_normals invert_face invert_surface invert_vertex read_canon_vertex_coordinates read_orig_vertex_coordinates read_pial_vertex_coordinates read_surface_vertex_set read_white_vertex_coordinates set_current_vertex_set show_surf shrink swap_vertex_fields
Cursor Operations
draw_cursor resend_to_subject select_orig_vertex_coordinates select_talairach_point select_vertex_by_vno send_spherical_point send_to_subject
Ripping and Cutting Operations
clear_ripflags cut_line cut_plane dilate_ripped restore_ripflags rip_all_vertices_except_contiguous_upripped undo_last_action
Reporting Information
dump_vertex get_selected_path_vnos labl_print_list labl_print_table plot_curv
Screen Shots
save_rgb save_rgb_cmp_frame save_tiff
Marking Operations
clear_all_vertex_marks clear_vertex_marks close_marked_vertices get_selected_path_vnos labl_mark_vertices labl_new_from_marked_vertices mark_annotation mark_contiguous_vertices_over_thresh mark_contiguous_vertices_with_similar_curvature mark_face mark_faces mark_vertex rip_all_vertices_except_contiguous_upripped val_to_mark
Label Operations
label_to_stat labl_dilate labl_erode labl_export_annotation labl_import_annotation labl_load labl_load_color_table labl_mark_vertices labl_new_from_marked_vertices labl_print_list labl_print_table labl_remove labl_remove_all labl_save labl_save_all labl_select labl_set_color labl_set_info labl_set_name_from_table labl_select_label_by_vno mask_label send_current_labels
Time Courses
func_clear_selection func_graph_timecourse_selection func_load_timecourse func_load_timecourse_offset func_print_timecourse_selection func_select_label func_select_marked_vertices
Paths
path_new_path_from_marked_vertices path_remove_selected_path path_select
Unsupported Functions
These commands are legacy functions that aren't documented well enough to be dependable. Because some older scripts still use them, they are documented here for completion. Use of them is not suggested nor supported.
Commands
add_subject_to_average_curvim subjectName morphSubdirectory
clear_all_vertex_cursor
compute_angles
compute_CMF
compute_cortical_thickness
compute_fieldsign
compute_pval_fwd pvalThreshold
pvalThreshold is a floating point number.
compute_pval_inv
compute_select_fwd maximumDistance
maximumDistance is a floating point number in millimeters.
compute_timecourses
curv_shrink_to_fill numberOfSteps
curv_to_curvim
curvim_to_second_surface
curvim_to_surface
deconvolve_weights weightFileName scaleFileName
draw_all_cursor
draw_all_vertex_cursor
draw_curvature_line
draw_fundus
draw_radius
draw_theta
draw_vector fileName
Reads an x/y vector from fileName and draws it to the screen.
ellipsoid_morph numberOfSteps rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
numberOfSteps is an integer. All distances are in millimeters and should be millimeters.
ellipsoid_project rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
- All distances are in millimeters and should be millimeters.
ellipsoid_shrink numberOfSteps radius
radius is in millimeters.
ellipsoid_shrink_bug numberOfSteps radius length
radius and length is in millimeters.
f_to_p DOFnumerator DOFdenominator
flatten
Reads the file name from subjtmpdir.
fill_second_surface
filter_recs
load_gcsa fileName
load_vals_from_sol tmid dt condition
tmid is the midpoint, dt is the delta to go on either side, and condition is the condition to use.
load_var_from_sol condition
condition is an integer.
make_lateral_view_second
normalize_area
normalize_binary_curv
normalize_inverse
normalize_second_binary_curv
normalize_time_courses type
type should be 0 to set all values to 1, 1 for normalizing for baseline noise covariance, 2 for normalizing for white noise, 3 for normalizing by read noise covariance matrix, and 4 for unity gain.
open_window
orient_sphere
plot_all_time_courses
plot_marked fileName
Generates a summary file of data from all marked vertices in fileName.
put_retinotopy_stats_in_vals
- Calculates retinotopy values at each vertex and stores them in the first overlay layer.
read_and_color_labeled_vertices red green blue
- Sets the meshr,g,b values and calls read_labeled_vertices. The colors are integers from 0-254.
read_and_smooth_parcellation parcellationFileName colorTableFileName soapBubbleIterations modeFilterIterations
Reads a parcellation from parcellationFileName using colorTableFileName and performs soap bubble and mode filter on the values.
read_annotated_image
Will read the file from annot.
read_curv_images
- Loads files into the curvim array.
read_disc subjectName
read_iop fileName dipoleFileNumber
read_ncov fileName
read_parcellation parcellationFileName colorTableFileName
- Reads and smooths a parcellation file into the annotation field. This is different than importing a parcellation file in as a series of labels; this parcellation goes right into surface value fields.
read_plot_list fileName
read_rec fileName
read_second_binary_curv
Reads a curvature file into mris2. Reads the file name from targcurv.
read_second_binary_surf
Reads mris2. Reads the file name from targsurf.
read_soltimecourse fileName
read_stds conditionNumber
- Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field.
read_surf fileName
- Reads only vertex positions from a file into the main surface, overwriting the original positions.
read_vertex_list fileName
really_align_brain
- Aligns first surface to second.
really_center_second_brain
- Works on the second mris.
redraw_second
- Draws second surface.
remove_triangle_links
Calls MRISremoveTriangleLinks.
restore_surf
- Restores the vertex positions in the temp position to the main position.
save_surf
- Saves the vertex positions in the main position to the temp position.
sclv_read_from_dotw_frame
- This seems to load in a surface full of values, and then individual values, from a file.
second_surface_curv_to_curvim
- Works on mris2.
shift_values
- Places the values from the first overlay field into the second.
smooth_curvim numberOfSteps
smooth_curvim_sparse numberOfSteps
sphere_shrink numberOfSteps radius
radius is in millimeters.
smooth_fs numberOfSteps
Smooths the field sign values by numberOfSteps, an integer.
smooth_val numberOfSteps
- sclv_smooth is used instead.
smooth_val_sparse numberOfSteps
sol_plot timePoint plotType
Uses the dlat value in computing the range.
subsample_dist spacing
Used in decimation. Calls MRISsubsampleDist. spacing is an integer.
subsample_orient spacing
Used in decimation. spacing is an integer.
swap_buffers
swap_curv
- Swaps the curv and curvbak fields.
swap_stat_val
- Swaps the values in the first overlay field and the fifth.
swap_val_val2
- Swaps the values in the first overlay field and the second.
swap_values
- Swaps the values in the first overlay field and the second.
t_to_p DOF
to_double_buffer
to_single_buffer
twocond condition condition
- Both conditions are integers.
write_binary_areas
Calls MRISwriteArea. Will read the file name from area.
write_binary_decimation
Calls MRISwriteDecimation. Will read the file name from dec.
write_binary_values
Calls MRISwriteValues. Will read the file name from val.
write_curv_images
Will read the file name from targcurvim.
write_decimation
Will read the file name from dec.
write_dipoles
Will read the file name from dip.
write_fill_images
write_subsample
Writes an ASCII file. Will read the file name from fs.
Index
add_subject_to_average_curvim clear_all_vertex_cursor compute_angles compute_CMF compute_cortical_thickness compute_fieldsign compute_pval_fwd compute_pval_inv compute_select_fwd compute_timecourses curv_shrink_to_fill curv_to_curvim curvim_to_second_surface curvim_to_surface deconvolve_weights draw_all_cursor draw_all_vertex_cursor draw_curvature_line draw_fundus draw_radius draw_theta draw_vector ellipsoid_morph ellipsoid_project ellipsoid_shrink ellipsoid_shrink_bug f_to_p flatten fill_second_surface filter_recs load_gcsa load_vals_from_sol load_var_from_sol make_lateral_view_second normalize_area normalize_binary_curv normalize_inverse normalize_second_binary_curv normalize_time_courses open_window orient_sphere plot_all_time_courses plot_marked put_retinotopy_stats_in_vals read_and_color_labeled_vertices read_and_smooth_parcellation read_annotated_image read_curv_images read_disc read_iop read_ncov read_parcellation read_plot_list read_rec read_second_binary_surf read_second_binary_curv read_soltimecourse read_stds read_surf read_vertex_list really_align_brain really_center_second_brain redraw_second remove_triangle_links restore_surf save_surf sclv_read_from_dotw_frame second_surface_curv_to_curvim shift_values smooth_curvim smooth_curvim_sparse sphere_shrink smooth_fs smooth_val smooth_val_sparse sol_plot subsample_dist subsample_orient swap_buffers swap_curv swap_stat_val swap_stat_val2 swap_values t_to_p to_single_buffer to_double_buffer twocond write_binary_areas write_binary_decimation write_binary_values write_curv_images write_decimation write_dipoles write_fill_images write_subsample
Notes
Any command with a * is only available in the internal dev version. If you need a copy of tksurfer with a command only available in the dev version, let the relevant people know