Deletions are marked like this. | Additions are marked like this. |
Line 853: | Line 853: |
=== Viewing Operations === [#align_sphere align_sphere] [#do_lighting_model do_lighting_model] [#draw_cursor draw_cursor] [#left_click left_click] [#make_lateral_view make_lateral_view] [#move_window move_window] |
|
Line 854: | Line 862: |
[#shrink shrink] [#smooth_curv smooth_curv] [#read_binary_surf read_binary_surf] [#show_surf show_surf] [#read_binary_curv read_binary_curv] [#read_binary_sulc read_binary_sulc] [#read_binary_values read_binary_values] [#read_binary_values_frame read_binary_values_frame] [#read_annotations read_annotations] [#read_binary_patch read_binary_patch] [#read_fieldsign read_fieldsign] [#read_fsmask read_fsmask] [#write_binary_surface write_binary_surface] [#write_binary_curv write_binary_curv] [#write_binary_sulc write_binary_sulc] [#write_binary_patch write_binary_patch] [#write_labeled_vertices write_labeled_vertices] [#read_labeled_vertices read_labeled_vertices] [#write_fieldsign write_fieldsign] [#write_fsmask write_fsmask] [#write_vrml write_vrml] [#write_binary_dipoles write_binary_dipoles] [#compute_curvature compute_curvature] [#clear_curvature clear_curvature] [#clear_ripflags clear_ripflags] [#restore_ripflags restore_ripflags] [#dilate_ripped dilate_ripped] [#cut_line cut_line] [#plot_curv plot_curv] [#cut_plane cut_plane] [#swap_val_val2 swap_val_val2] [#save_rgb save_rgb] [#save_rgb_cmp_frame save_rgb_cmp_frame] |
|
Line 890: | Line 865: |
[#scale_brain scale_brain] [#send_current_labels send_current_labels] [#show_flat_regions show_flat_regions] |
|
Line 893: | Line 871: |
[#scale_brain scale_brain] [#resize_window resize_window] [#move_window move_window] [#do_lighting_model do_lighting_model] [#restore_zero_position restore_zero_position] [#restore_initial_position restore_initial_position] [#make_lateral_view make_lateral_view] |
[#read_really_matrix read_really_matrix] |
Line 901: | Line 873: |
[#write_view_matrix write_view_matrix] [#read_really_matrix read_really_matrix] [#write_really_matrix write_really_matrix] [#really_translate_brain really_translate_brain] [#really_scale_brain really_scale_brain] |
[#really_center_brain really_center_brain] |
Line 909: | Line 877: |
[#align_sphere align_sphere] [#really_center_brain really_center_brain] |
[#really_scale_brain really_scale_brain] [#really_translate_brain really_translate_brain] [#resize_brain resize_brain] [#resize_window resize_window] [#restore_zero_position restore_zero_position] [#restore_initial_position restore_initial_position] [#transform_brain transform_brain] [#write_view_matrix write_view_matrix] [#write_really_matrix write_really_matrix] === I/O === [#func_load_timecourse func_load_timecourse] [#func_load_timecourse_offset func_load_timecourse_offset] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_save labl_save] [#labl_save_all labl_save_all] [#read_annotations read_annotations] [#read_binary_curv read_binary_curv] |
Line 913: | Line 901: |
[#read_binary_sulc read_binary_sulc] [#read_binary_surf read_binary_surf] [#read_binary_values read_binary_values] [#read_binary_values_frame read_binary_values_frame] [#read_binary_patch read_binary_patch] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_curv_to_val read_curv_to_val] [#read_fieldsign read_fieldsign] [#read_fsmask read_fsmask] [#read_imag_vals read_imag_vals] [#read_labeled_vertices read_labeled_vertices] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_write_dotw sclv_write_dotw] [#write_binary_curv write_binary_curv] [#write_binary_dipoles write_binary_dipoles] [#write_binary_patch write_binary_patch] [#write_binary_surface write_binary_surface] [#write_binary_sulc write_binary_sulc] [#write_fieldsign write_fieldsign] [#write_fsmask write_fsmask] [#write_labeled_vertices write_labeled_vertices] [#write_vrml write_vrml] === Curvature Operations === [#clear_curvature clear_curvature] [#compute_curvature compute_curvature] [#curv_to_val curv_to_val] [#fill_flood_from_cursor fill_flood_from_cursor] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#smooth_curv smooth_curv] [#val_to_curv val_to_curv] === Overlay Operations === [#curv_to_val curv_to_val] [#f_to_t f_to_t] [#fill_flood_from_cursor fill_flood_from_cursor] [#label_to_stat label_to_stat] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#sclv_copy_all_view_settings_from_current_field sclv_copy_all_view_settings_from_current_field] [#sclv_copy_view_settings_from_current_field sclv_copy_view_settings_from_current_field] [#sclv_copy_view_settings_from_field sclv_copy_view_settings_from_field] [#sclv_get_normalized_color_for_value sclv_get_normalized_color_for_value] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_send_current_field_info sclv_send_current_field_info] [#sclv_send_histogram sclv_send_histogram] [#sclv_set_current_field sclv_set_current_field] [#sclv_set_current_threshold_from_percentile sclv_set_current_threshold_from_percentile] [#sclv_set_current_threshold_using_fdr sclv_set_current_threshold_using_fdr] [#sclv_set_current_timepoint sclv_set_current_timepoint] [#sclv_set_overlay_alpha sclv_set_overlay_alpha] [#sclv_smooth sclv_smooth] [#sclv_write_dotw sclv_write_dotw] [#stat_to_val stat_to_val] [#swap_val_val2 swap_val_val2] [#val_to_curv val_to_curv] [#val_to_stat val_to_stat] === Vertex Operations === [#fill_flood_from_cursor fill_flood_from_cursor] |
|
Line 914: | Line 978: |
[#fix_nonzero_vals fix_nonzero_vals] [#flip_normals flip_normals] [#invert_face invert_face] [#invert_surface invert_surface] [#invert_vertex invert_vertex] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#set_current_vertex_set set_current_vertex_set] [#show_surf show_surf] [#shrink shrink] [#swap_vertex_fields swap_vertex_fields] === Cursor Operations === [#draw_cursor draw_cursor] [#resend_to_subject resend_to_subject] |
|
Line 916: | Line 999: |
[#read_white_vertex_coordinates read_white_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] |
[#select_vertex_by_vno select_vertex_by_vno] |
Line 922: | Line 1002: |
[#resend_to_subject resend_to_subject] [#invert_surface invert_surface] [#fix_nonzero_vals fix_nonzero_vals] [#invert_vertex invert_vertex] [#invert_face invert_face] |
=== Ripping and Cutting Operations === [#clear_ripflags clear_ripflags] [#cut_line cut_line] [#cut_plane cut_plane] [#dilate_ripped dilate_ripped] [#restore_ripflags restore_ripflags] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] [#undo_last_action undo_last_action] === Reporting Information === [#dump_vertex dump_vertex] [#get_selected_path_vnos get_selected_path_vnos] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#plot_curv plot_curv] === Screen Shots === [#save_rgb save_rgb] [#save_rgb_cmp_frame save_rgb_cmp_frame] [#save_tiff save_tiff] === Marking Operations === [#clear_all_vertex_marks clear_all_vertex_marks] [#clear_vertex_marks clear_vertex_marks] [#close_marked_vertices close_marked_vertices] [#get_selected_path_vnos get_selected_path_vnos] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] |
Line 928: | Line 1036: |
[#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#mark_face mark_face] |
|
Line 929: | Line 1040: |
[#mark_face mark_face] [#dump_vertex dump_vertex] |
[#mark_vertex mark_vertex] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] |
Line 932: | Line 1043: |
[#resize_brain resize_brain] [#transform_brain transform_brain] [#show_flat_regions show_flat_regions] [#val_to_stat val_to_stat] [#stat_to_val stat_to_val] [#read_imag_vals read_imag_vals] [#f_to_t f_to_t] |
=== Label Operations === |
Line 940: | Line 1047: |
[#val_to_curv val_to_curv] [#curv_to_val curv_to_val] [#read_curv_to_val read_curv_to_val] |
[#labl_dilate labl_dilate] [#labl_erode labl_erode] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#labl_remove labl_remove] [#labl_remove_all labl_remove_all] [#labl_save labl_save] [#labl_save_all labl_save_all] [#labl_select labl_select] [#labl_set_color labl_set_color] [#labl_set_info labl_set_info] [#labl_set_name_from_table labl_set_name_from_table] [#labl_select_label_by_vno labl_select_label_by_vno] |
Line 944: | Line 1067: |
[#dump_faces dump_faces] [#left_click left_click] [#draw_cursor draw_cursor] [#mark_vertex mark_vertex] |
|
Line 949: | Line 1068: |
[#select_vertex_by_vno select_vertex_by_vno] [#swap_vertex_fields swap_vertex_fields] [#clear_vertex_marks clear_vertex_marks] [#clear_all_vertex_marks clear_all_vertex_marks] [#close_marked_vertices close_marked_vertices] [#undo_last_action undo_last_action] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_write_dotw sclv_write_dotw] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_smooth sclv_smooth] [#sclv_set_overlay_alpha sclv_set_overlay_alpha] [#sclv_set_current_field sclv_set_current_field] [#sclv_set_current_timepoint sclv_set_current_timepoint] [#sclv_copy_view_settings_from_current_field sclv_copy_view_settings_from_current_field] [#sclv_copy_all_view_settings_from_current_field sclv_copy_all_view_settings_from_current_field] [#sclv_copy_view_settings_from_field sclv_copy_view_settings_from_field] [#sclv_set_current_threshold_from_percentile sclv_set_current_threshold_from_percentile] [#sclv_set_current_threshold_using_fdr sclv_set_current_threshold_using_fdr] [#sclv_send_histogram sclv_send_histogram] [#sclv_send_current_field_info sclv_send_current_field_info] [#sclv_get_normalized_color_for_value sclv_get_normalized_color_for_value] [#read_surface_vertex_set read_surface_vertex_set] [#set_current_vertex_set set_current_vertex_set] |
=== Time Courses === [#func_clear_selection func_clear_selection] [#func_graph_timecourse_selection func_graph_timecourse_selection] |
Line 978: | Line 1075: |
[#func_print_timecourse_selection func_print_timecourse_selection] [#func_select_label func_select_label] |
|
Line 979: | Line 1078: |
[#func_select_label func_select_label] [#func_clear_selection func_clear_selection] [#func_graph_timecourse_selection func_graph_timecourse_selection] [#func_print_timecourse_selection func_print_timecourse_selection] [#labl_load_color_table labl_load_color_table] [#labl_load labl_load] [#labl_save labl_save] [#labl_save_all labl_save_all] [#labl_import_annotation labl_import_annotation] [#labl_export_annotation labl_export_annotation] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#labl_mark_vertices labl_mark_vertices] [#labl_select labl_select] [#labl_set_name_from_table labl_set_name_from_table] [#labl_set_info labl_set_info] [#labl_set_color labl_set_color] [#labl_remove labl_remove] [#labl_remove_all labl_remove_all] [#labl_erode labl_erode] [#labl_dilate labl_dilate] [#labl_select_label_by_vno labl_select_label_by_vno] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#path_select path_select] |
=== Paths === |
Line 1005: | Line 1083: |
[#fill_flood_from_cursor fill_flood_from_cursor] [#get_marked_vnos get_marked_vnos] [#get_selected_path_vnos get_selected_path_vnos] [#save_tiff save_tiff] [#flip_normals flip_normals] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] |
[#path_select path_select] |
Line 1019: | Line 1091: |
??? Not used in tksurfer.tcl. Looks like it probably caused a crash anyways (fixed). [[Anchor(area_shrink)]] ''area_shrink'' '''''numberOfSteps''''' ??? Not used, code is commented out. |
|
Line 1029: | Line 1094: |
??? Clears all the vertex_plotlist cursors. |
|
Line 1034: | Line 1097: |
??? Not used in tksurfer.tcl. |
|
Line 1039: | Line 1100: |
??? Not used in tksurfer.tcl. |
|
Line 1044: | Line 1103: |
??? Not used int tksurfer.tcl. |
|
Line 1049: | Line 1106: |
??? Not used in tksurfer.tcl. Sets the field sign and field sign mask values in the surface. |
|
Line 1054: | Line 1109: |
??? Not used in tksurfer.tcl. '''pvalThreshold''' is a floating point number. | '''pvalThreshold''' is a floating point number. |
Line 1059: | Line 1114: |
??? Not used in tksurfer.tcl. |
|
Line 1064: | Line 1117: |
??? Not used in tksurfer.tcl. | |
Line 1070: | Line 1122: |
??? Not used in tksurfer.tcl. |
|
Line 1075: | Line 1125: |
??? Unused in tksurfer.tcl. |
|
Line 1080: | Line 1128: |
??? Not used in tksurfer.tcl. |
|
Line 1085: | Line 1131: |
??? Not used in tksurfer.tcl. Works on mris2. |
|
Line 1090: | Line 1134: |
??? Not used in tksurfer.tcl. Appears to convert a value from curvim to curv vertex field. |
|
Line 1095: | Line 1137: |
??? Not used in tksurfer.tcl. |
|
Line 1100: | Line 1140: |
??? Draws all the sol_nplotlist points as cursors. |
|
Line 1105: | Line 1143: |
??? Draws all the vertex_plotlist points as cursors. |
|
Line 1110: | Line 1146: |
??? Not used in tksurfer.tcl. |
|
Line 1115: | Line 1149: |
??? Not used in tksurfer.tcl. |
|
Line 1120: | Line 1152: |
??? Not used in tksurfer.tcl. |
|
Line 1125: | Line 1155: |
??? Not used in tksurfer.tcl. |
|
Line 1130: | Line 1158: |
??? Not used in tksurfer.tcl. Reads an x/y vector from '''fileName''' and draws it to the screen. | Reads an x/y vector from '''fileName''' and draws it to the screen. |
Line 1135: | Line 1163: |
??? Unused in tksurfer.tcl. All distances are in radius. | '''numberOfSteps''' is an integer. All distances are in millimeters and should be millimeters. |
Line 1140: | Line 1168: |
??? Unused in tksurfer.tcl All distances are in radius. | All distances are in millimeters and should be millimeters. |
Line 1145: | Line 1173: |
??? Unused in tksurfer.tcl. '''radius''' is in millimeters. | '''radius''' is in millimeters. |
Line 1150: | Line 1178: |
??? Unused in tksurfer.tcl. '''radius''' and '''length''' is in millimeters. | '''radius''' and '''length''' is in millimeters. |
Line 1155: | Line 1183: |
??? Not used in tksurfer.tcl. |
|
Line 1160: | Line 1186: |
??? Not used in tksurfer.tcl. Reads the file name from subjtmpdir. | Reads the file name from '''subjtmpdir'''. |
Line 1165: | Line 1191: |
??? Not used in tksurfer.tcl. |
|
Line 1170: | Line 1194: |
??? Not used in tksurfer.tcl. |
|
Line 1175: | Line 1197: |
??? Calls GCSAread. |
|
Line 1180: | Line 1200: |
??? Not used in tksurfer.tcl. '''tmid''' is the midpoint, '''dt''' is the delta to go on either side, and '''condition''' is the condition to use. | '''tmid''' is the midpoint, '''dt''' is the delta to go on either side, and '''condition''' is the condition to use. |
Line 1185: | Line 1205: |
??? Not used in tksurfer.tcl '''condition''' is an integer. | '''condition''' is an integer. |
Line 1190: | Line 1210: |
??? Not used in tksurfer.tcl. Sets the view for the second surface. |
|
Line 1195: | Line 1213: |
??? Not used in tksurfer.tcl. |
|
Line 1200: | Line 1216: |
??? Not used in tksurfer.tcl. |
|
Line 1205: | Line 1219: |
??? Not used in tksurfer.tcl. |
|
Line 1210: | Line 1222: |
??? Not used in tksurfer.tcl. Works on mris2. |
|
Line 1215: | Line 1225: |
??? Not used in tksurfer.tcl. '''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. | '''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. |
Line 1220: | Line 1230: |
??? Used in older scripts, but not needed any more. |
|
Line 1225: | Line 1233: |
??? Not used in tksurfer.tcl. |
|
Line 1230: | Line 1236: |
??? Not used in tksurfer.tcl. |
|
Line 1235: | Line 1239: |
??? Generates a summary file of data from all marked vertices in '''fileName'''. | Generates a summary file of data from all marked vertices in '''fileName'''. |
Line 1240: | Line 1244: |
??? Not used in tksurfer.tcl. Calculates retinotopy values at each vertex and stores them in the first overlay layer. | Calculates retinotopy values at each vertex and stores them in the first overlay layer. |
Line 1245: | Line 1249: |
??? Not used in tksurfer.tcl. Sets the meshr,g,b values and calls read_labeled_vertices. The colors are integers from 0-254. | Sets the meshr,g,b values and calls read_labeled_vertices. The colors are integers from 0-254. |
Line 1250: | Line 1254: |
??? Reads a parcellation from '''parcellationFileName''' using '''colorTableFileName''' and performs soap bubble and mode filter on the values. | Reads a parcellation from '''parcellationFileName''' using '''colorTableFileName''' and performs soap bubble and mode filter on the values. |
Line 1255: | Line 1259: |
??? Not used in tksurfer.tcl. Will read the file from '''annot'''. | Will read the file from '''annot'''. |
Line 1260: | Line 1264: |
??? Not used in tksurfer.tcl. Loads files into the curvim array. | Loads files into the curvim array. |
Line 1265: | Line 1269: |
??? Not used in tksurfer.tcl. |
|
Line 1270: | Line 1272: |
??? Not used in tksurfer.tcl. |
|
Line 1275: | Line 1275: |
??? Not used in tksurfer.tcl. |
|
Line 1280: | Line 1278: |
??? 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. | 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. |
Line 1285: | Line 1283: |
??? Not used in tksurfer.tcl. Reads into sol_nplotlist. |
|
Line 1290: | Line 1286: |
??? Not used in tksurfer.tcl. |
|
Line 1295: | Line 1289: |
??? Not used in tksurfer.tcl. Reads a curvature file into mris2. Reads the file name from '''targcurv'''. | Reads a curvature file into mris2. Reads the file name from '''targcurv'''. |
Line 1300: | Line 1294: |
??? Not used in tksurfer.tcl. Reads mris2. Reads the file name from '''targsurf'''. | Reads mris2. Reads the file name from '''targsurf'''. |
Line 1305: | Line 1299: |
??? Not used in tksurfer.tcl. |
|
Line 1310: | Line 1302: |
??? Not used in tksurfer.tcl. Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field. | Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field. |
Line 1315: | Line 1307: |
??? Not used in tksurfer.tcl. Reads only vertex positions from a file into the main surface, overwriting the original positions. | Reads only vertex positions from a file into the main surface, overwriting the original positions. |
Line 1320: | Line 1312: |
??? Not used in tksurfer.tcl. Reads into vertex_plotlist. |
|
Line 1325: | Line 1315: |
??? Not used in tksurfer.tcl. Aligns first surface to second. | Aligns first surface to second. |
Line 1330: | Line 1320: |
??? Not used in tksurfer.tcl. Works on the second mris. | Works on the second mris. |
Line 1335: | Line 1325: |
??? Looks like it redraws the 'second surface'. Maybe not used any more? | Draws second surface. |
Line 1340: | Line 1330: |
??? Calls MRI``Sremove``Triangle``Links. | Calls MRI``Sremove``Triangle``Links. |
Line 1345: | Line 1335: |
??? Not used in tksurfer.tcl. Restores the vertex positions in the temp position to the main position. | Restores the vertex positions in the temp position to the main position. |
Line 1350: | Line 1340: |
??? Not used in tksurfer.tcl. Saves the vertex positions in the main position to the temp position. | Saves the vertex positions in the main position to the temp position. |
Line 1355: | Line 1345: |
??? This seems to load in a surface full of values, and then individual values, from a file. | This seems to load in a surface full of values, and then individual values, from a file. |
Line 1360: | Line 1350: |
??? Not used in tksurfer.tcl. Works on mris2. | Works on mris2. |
Line 1365: | Line 1355: |
??? Not used in tksurfer.tcl. Places the values from the first overlay field into the second. | Places the values from the first overlay field into the second. |
Line 1370: | Line 1360: |
??? Unused in tksurfer.tcl. |
|
Line 1375: | Line 1363: |
??? Not used in tksurfer.tcl. |
|
Line 1380: | Line 1366: |
??? Unused in tksurfer.tcl. '''radius''' is in millimeters. | '''radius''' is in millimeters. |
Line 1385: | Line 1371: |
??? Not used in tksurfer.tcl. Smooths the field sign values by '''numberOfSteps''', an integer. | Smooths the field sign values by '''numberOfSteps''', an integer. |
Line 1390: | Line 1376: |
??? Not used in tksurfer.tcl; sclv_smooth is used instead. | sclv_smooth is used instead. |
Line 1395: | Line 1381: |
??? Not used in tksurfer.tcl. |
|
Line 1400: | Line 1384: |
??? Not used in tksurfer.tcl. Uses the '''dlat''' value in computing the range. | Uses the '''dlat''' value in computing the range. |
Line 1405: | Line 1389: |
??? Used in decimation. Calls MRI``Ssubsample``Dist. '''spacing''' is an integer. | Used in decimation. Calls MRI``Ssubsample``Dist. '''spacing''' is an integer. |
Line 1410: | Line 1394: |
??? Used in decimation. '''spacing''' is an integer. | Used in decimation. '''spacing''' is an integer. |
Line 1415: | Line 1399: |
??? Unused in tksurfer.tcl |
|
Line 1420: | Line 1402: |
??? Not used in tksurfer.tcl. Swaps the curv and curvbak fields. | Swaps the curv and curvbak fields. |
Line 1425: | Line 1407: |
??? Not used in tksurfer.tcl. Swaps the values in the first overlay field and the fifth. | Swaps the values in the first overlay field and the fifth. |
Line 1430: | Line 1412: |
??? Not used in tksurfer.tcl. Swaps the values in the first overlay field and the second. | Swaps the values in the first overlay field and the second. |
Line 1435: | Line 1417: |
??? Not used in tksurfer.tcl. Swaps the values in the first overlay field and the second. | Swaps the values in the first overlay field and the second. |
Line 1440: | Line 1422: |
??? Not used in tksurfer.tcl. |
|
Line 1445: | Line 1425: |
??? Unused in tksurfer.tcl |
|
Line 1450: | Line 1428: |
??? Unused in tksurfer.tcl |
|
Line 1455: | Line 1431: |
??? Not used in tksurfer.tcl. Both conditions are integers. | Both conditions are integers. |
Line 1460: | Line 1436: |
??? Not used in tksurfer.tcl. Calls MRI``Swrite``Area. Will read the file name from '''area'''. | Calls MRI``Swrite``Area. Will read the file name from '''area'''. |
Line 1465: | Line 1441: |
??? Calls MRI``Swrite``Decimation. Will read the file name from '''dec'''. | Calls MRI``Swrite``Decimation. Will read the file name from '''dec'''. |
Line 1470: | Line 1446: |
??? Not used in tksurfer.tcl. Calls MRI``Swrite``Values. Will read the file name from '''val'''. | Calls MRI``Swrite``Values. Will read the file name from '''val'''. |
Line 1475: | Line 1451: |
??? Not used in tksurfer.tcl. Will read the file name from '''targcurvim'''. | Will read the file name from '''targcurvim'''. |
Line 1480: | Line 1456: |
??? Not used in tksurfer.tcl. Will read the file name from '''dec'''. | Will read the file name from '''dec'''. |
Line 1485: | Line 1461: |
??? Not used in tksurfer.tcl. Will read the file name from '''dip'''. | Will read the file name from '''dip'''. |
Line 1490: | Line 1466: |
??? Not used in tksurfer.tcl. |
|
Line 1495: | Line 1469: |
??? Writes an ASCII file. Will read the file name from '''fs'''. |
Writes an ASCII file. Will read the file name from '''fs'''. === Index === |
Line 1498: | Line 1474: |
[#area_shrink area_shrink] |
Up to TkSurferGuide |
Back to [:../TkSurferScriptingReference: TkSurferScriptingReference] |
Continue to [:TkSurferGuide/TkSurferReference: TkSurferReference] |
Scripting
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.
Commands
Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional.
Anchor(align_sphere) 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).
Anchor(clear_all_vertex_marks) 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).
Anchor(clear_curvature) clear_curvature
- Sets all curvature values to 0.
Anchor(clear_ripflags) clear_ripflags
- Unrips all vertices.
Anchor(clear_vertex_marks) clear_vertex_marks
- Unmarks the marked vertices.
Anchor(close_marked_vertices) close_marked_vertices
- Adds the first marked vertex to the end of the list of marked vertices.
Anchor(compute_curvature) compute_curvature
- Computes the curvature based on vertex positions.
Anchor(curv_to_val) curv_to_val
- Copies the curvature values into the first overlay values.
Anchor(cut_line) 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.
Anchor(cut_plane) cut_plane
- Cuts a plane based on four marked vertices: three to define the plane, and one to indicate which area to not cut.
Anchor(dilate_ripped) dilate_ripped
- Dilates ripped areas, increasing their size by a vertex.
Anchor(do_lighting_model) 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.
Anchor(draw_cursor) draw_cursor vertexNumber on
Draws the specified vertex in blue if on, or in the background color if not on.
Anchor(dump_vertex) dump_vertex vertexNumber
Prints information about the specified vertex. vertexNumber is an integer.
Anchor(f_to_t) f_to_t
- Squares and takes the absolute value for every overlay value field in the vertices.
Anchor(find_orig_vertex_coordinates) find_orig_vertex_coordinates
Performs the Save Cursor function. Writes the current cursor location to the edit.dat file.
Anchor(fix_nonzero_vals) 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.
Anchor(flip_normals) 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.
Anchor(func_clear_selection) func_clear_selection
- Clears the functional time course selection.
Anchor(func_graph_timecourse_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.
Anchor(func_load_timecourse) 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.
Anchor(func_load_timecourse_offset) 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.
Anchor(func_print_timecourse_selection) func_print_timecourse_selection fileName
- Prints a text file summarizing the data selected in the functional time course.
Anchor(func_select_label) 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.
Anchor(func_select_marked_vertices) 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.
Anchor(invert_face) invert_face faceNumber
Inverts the face normal at the numbered face. faceNumber is an integer.
Anchor(fill_flood_from_cursor) 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. |
Anchor(get_marked_vnos) get_marked_vnos
- Returns a list of marked vertices.
Anchor(get_selected_path_vnos) get_selected_path_vnos
- Returns a list of vertices in the selected path.
Anchor(invert_surface) invert_surface
- Inverts the vertex normals for all unripped vertices in the surface, but not the faces.
Anchor(invert_vertex) invert_vertex vertexNumber
Inverts the vertex normal at the numbered vertex. vertexNumber is an integer.
Anchor(label_to_stat) label_to_stat overlayField
Creates a new overlay layer with the values in the current label in overlay field overlayField.
Anchor(labl_dilate) labl_dilate label
Expands a label by adding all vertices immediately adjacent to the label. label should be a valid label index.
Anchor(labl_erode) labl_erode label
Shrinks a label by excluding all border vertices in the label. label should be a valid label index.
Anchor(labl_export_annotation) labl_export_annotation fileName
- Exports all labels marked as structures to an annotation.
Anchor(labl_import_annotation) labl_import_annotation fileName
- Important an annotation file as a series of label.
Anchor(labl_load) labl_load fileName
Loads the label in fileName and adds it to the Labels window.
Anchor(labl_load_color_table) labl_load_color_table fileName
Loads a color table for labels to use from fileName.
Anchor(labl_mark_vertices) labl_mark_vertices label
Marks the vertices in a label. label should be a valid label index.
Anchor(labl_new_from_marked_vertices) labl_new_from_marked_vertices
- Creates a new label from the marked vertices.
Anchor(labl_print_list) labl_print_list
- Prints a list of label information to the shell
Anchor(labl_print_table) labl_print_table
- Prints the color table to the shell.
Anchor(labl_remove) labl_remove label
Deletes a label. label should be a valid label index.
Anchor(labl_remove_all) labl_remove_all
- Deletes all labels.
Anchor(labl_save) labl_save label fileName
Saves a label to fileName. label should be a valid label index.
Anchor(labl_save_all) labl_save_all prefix
- Saves all labels with a given prefix directory location.
Anchor(labl_select) labl_select label
Marks the vertices in a label. label should be a valid label index.
Anchor(labl_select_label_by_vno) 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.
Anchor(labl_set_color) 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.
Anchor(labl_set_info) 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.
Anchor(labl_set_name_from_table) 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.
Anchor(left_click) left_click x y
Simulates a click at the given window position. x and y should be integers.
Anchor(make_lateral_view) make_lateral_view
- Changes the view to show the surface laterally.
Anchor(mark_annotation) mark_annotation vertexNumber
Will mark all vertices with the same annotation value as the annotation value at the specified vertex. vertexNumber is an integer.
Anchor(mark_contiguous_vertices_over_thresh) 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.)
Anchor(mark_contiguous_vertices_with_similar_curvature) 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.)
Anchor(mark_face) mark_face faceNumber
Marks all vertices in the specified face. faceNumber is an integer.
Anchor(mark_faces) mark_faces vertexNumber
Marks all vertices in the face to which the specified vertex belongs. vertexNumber is an integer.
Anchor(mark_vertex) mark_vertex vertexNumber on
Marks or unmarks a specified vertex. vertexNumber is an integer, and on is 0 for off and 1 for on.
Anchor(mask_label) mask_label labelFileName
- This reads and marks a label file, and then for every vertex not marked, clears the overlay values.
Anchor(move_window) 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.
Anchor(path_new_path_from_marked_vertices) 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.
Anchor(path_remove_selected_path) path_remove_selected_path
- Deletes the selected path.
Anchor(path_select) path_select path
Selects the specified path. path should be a valid path index.
Anchor(plot_curv) 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.
Anchor(read_annotations) read_annotations fileName
Deprecated, replaced by labl_import_annotation. fileName is an annotation file name, usually ending in .annot.
Anchor(read_binary_curv) read_binary_curv
Loads a curvature file into the surface. Reads the file name from curv.
Anchor(read_binary_decimation) read_binary_decimation
Reads decimation values onto the surface from a file. Reads the file name from dec.
Anchor(read_binary_dipoles) read_binary_dipoles
Reads dipole balues onto the surface from a file. Reads the file name from dip.
Anchor(read_binary_patch) read_binary_patch
Reads a patch file into the surface. Will read the file name from patch.
Anchor(read_binary_sulc) read_binary_sulc
Reads a sulcus file into the curvature display. Reads the file name from sulc.
Anchor(read_binary_surf) read_binary_surf
Loads the main surface from a surface file. Reads the file name from insurf.
Anchor(read_binary_values) read_binary_values
Deprecated, replaced by sclv_read_from_dotw. Will read the value file from val.
Anchor(read_binary_values_frame) read_binary_values_frame
Deprecated, replaced by sclv_read_from_dotw_frame. Will read the value file from val.
Anchor(read_canon_vertex_coordinates) read_canon_vertex_coordinates fileName
- Reads the vertex coordinates from a file into the canonical vertex set.
Anchor(read_curv_to_val) read_curv_to_val fileName
- Reads a curvature file into the first overlay layer.
Anchor(read_fieldsign) read_fieldsign
Reads field sign values from a file. Will read the file name from fs.
Anchor(read_fsmask) read_fsmask
Reads the field sign mask from a file. Will read the file name from fm.
Anchor(read_imag_vals) read_imag_vals fileName
Reads imaginary values from fileName.
Anchor(read_labeled_vertices) read_labeled_vertices
Deprecated, replaced by labl_load. Will read the file name from label.
Anchor(read_orig_vertex_coordinates) read_orig_vertex_coordinates
Reads the vertex coordinates from a file into the orig vertex set. Reads the file name from origcoords.
Anchor(read_pial_vertex_coordinates) 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.
Anchor(read_really_matrix) read_really_matrix
Reads a matrix to transform the surface vertices. Reads the file name from subjtmpdir.
Anchor(read_surface_vertex_set) 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 |
Anchor(read_view_matrix) read_view_matrix
Reads a view matrix from a file. Reads the file name from subjtmpdir.
Anchor(read_white_vertex_coordinates) read_white_vertex_coordinates
Reads the vertex coordinates from a file called ?h.white where ? is the current hemisphere into the original vertex set.
Anchor(really_center_brain) really_center_brain
- Translates the surface coordinates to an average of all vertex coordinates.
Anchor(really_rotate_brain_x) really_rotate_brain_x degrees
Rotates the surface vertices around the x axis. degrees is a floating point number.
Anchor(really_rotate_brain_y) really_rotate_brain_y degrees
Rotates the surface vertices around the y axis. degrees is a floating point number.
Anchor(really_rotate_brain_z) really_rotate_brain_z degrees
Rotates the surface vertices around the z axis. degrees is a floating point number.
Anchor(really_translate_brain) really_translate_brain rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
- Translates the surface vertices along the specified axes. All distances are in millimeters and can be floating point.
Anchor(redraw) redraw
- Redraws the graphics window. It is necessary to call this after using other script commands to change the viewing state.
Anchor(resend_to_subject) resend_to_subject
Calls send_to_subject with the sam subject name used in the previous send_to_subject call.
Anchor(resize_brain) resize_brain
- Scales the brain according to the surface area to total area ratio.
Anchor(resize_window) resize_window size
Resizes the graphics window. size is an integer. The new window size will be sqaure with size x sizedimensions.
Anchor(restore_ripflags) 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.
Anchor(restore_initial_position) restore_initial_position
- Restores the view to a medial view.
Anchor(restore_zero_position) restore_zero_position
- Restores the view to a medial view.
Anchor(rip_all_vertices_except_contiguous_upripped) 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.)
Anchor(rotate_brain_x) rotate_brain_x degrees
Rotates the view around the x axis. degrees should be a floating point number.
Anchor(rotate_brain_y) rotate_brain_y degrees
Rotates the view around the y axis. degrees should be a floating point number.
Anchor(rotate_brain_z) rotate_brain_z degrees
Rotates the view around the z axis. degrees should be a floating point number.
Anchor(save_rgb) save_rgb
Saves the contents of the view to a file in RGB format. Reads the file name from rgb.
Anchor(save_rgb_cmp_frame) save_rgb_cmp_frame
Reads the file name from rgb. Write an rgb frame file to be composed into a movie later.
Anchor(save_tiff) save_tiff fileName
- Saves the current graphics contents as a TIFF file.
Anchor(scale_brain) 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.
Anchor(sclv_copy_all_view_settings_from_current_field) sclv_copy_all_view_settings_from_current_field
- Copies the settings from the current overlay to all other overlay layers.
Anchor(sclv_copy_view_settings_from_current_field) 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.
Anchor(sclv_copy_view_settings_from_field) 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.
Anchor(sclv_get_normalized_color_for_value) 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.
Anchor(sclv_load_label_value_file) 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.
Anchor(sclv_read_bfile_values) sclv_read_bfile_values
Deprecated, replaced by sclv_read_from_volume.
Anchor(sclv_read_binary_values) sclv_read_binary_values
Deprecated, replaced by sclv_read_from_dotw.
Anchor(sclv_read_binary_values_frame) sclv_read_binary_values_frame fileName field
Deprecated, replaced by sclv_read_from_dotw_frame.
Anchor(sclv_read_from_dotw) 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 |
Anchor(sclv_read_from_volume) 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.
Anchor(sclv_send_histogram) 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.
Anchor(sclv_send_current_field_info) 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.
Anchor(sclv_set_current_field) 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.
Anchor(sclv_set_current_threshold_from_percentile) 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 0-100 representing percentages which will be mapped to overlay values to be used to set the threshold.
Anchor(sclv_set_current_threshold_using_fdr) 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.
Anchor(sclv_set_current_timepoint) 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.
Anchor(sclv_set_overlay_alpha) 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.
Anchor(sclv_smooth) 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.
Anchor(sclv_write_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.
Anchor(select_orig_vertex_coordinates) select_orig_vertex_coordinates
Performs the Read Cursor function. Reads the cursor location from the edit.dat file.
Anchor(select_talairach_point) 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.
Anchor(select_vertex_by_vno) select_vertex_by_vno vertexNumber
Selects the given vertex as the cursor. vertexNumber is an integer.
Anchor(send_current_labels) 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.
Anchor(send_spherical_point) 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.
Anchor(send_to_subject) send_to_subject subjectName
Calls send_sphericAnchor(curv_to_val)
curv_to_val al_point
Anchor(set_current_vertex_set) 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.
Anchor(show_flat_regions) 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.
Anchor(show_surf) show_surf vertexSet
Moves the specified vertex set into the main vertex set position. vertexSet is white, pial, or inflate.
Anchor(shrink) shrink numberOfSteps
Inflates the surface by the number of steps given. numberOfSteps should be an integer.
Anchor(smooth_curv) smooth_curv numberOfSteps
Smooths the curvature values by numberOfSteps, an integer
Anchor(stat_to_val) stat_to_val
- Copies the values of the stat field to the overlay value field.
Anchor(swap_vertex_fields) 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 |
Anchor(transform_brain) transform_brain
- Recenters the brain.
Anchor(translate_brain_x) translate_brain_x distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
Anchor(translate_brain_y) translate_brain_y distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
Anchor(translate_brain_z) translate_brain_z distance
Translates the view along the x axis. distance should be a floating point number and is in millimeters.
Anchor(undo_last_action) undo_last_action
- Undoes the last action.
Anchor(val_to_curv) val_to_curv
- Copies the first overlay values into the curvature values.
Anchor(val_to_mark) val_to_mark
- Will mark all vertices with overlay values greater than the overlay threshold.
Anchor(val_to_stat) val_to_stat
- Copies the values of the overlay value field to the stat field.
Anchor(write_binary_curv) write_binary_curv
Saves the curvature values to a new file. Will read the file name from curv.
Anchor(write_binary_dipoles) write_binary_dipoles
Write the dipoles to a file. Will read the file name from dip.
Anchor(write_binary_patch) write_binary_patch
Saves the current surface as a patch. Will read the file name from patch.
Anchor(write_binary_sulc) write_binary_sulc
Saves the sulcus values (if loaded in the curvature set) to a new file. Will read the file name from sulc.
Anchor(write_binary_surface) write_binary_surface
Saves the surface to a new file. Will read the file name from outsurf.
Anchor(write_fieldsign) write_fieldsign
Saves the field sign values to a new file. Will read the file name from fs.
Anchor(write_fsmask) write_fsmask
Saves the field sign mask to a new file. Will read the file name from fm.
Anchor(write_labeled_vertices) 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.
Anchor(write_really_matrix) write_really_matrix
Writes the matrix used to transform the surface vertices. Reads the file name from subjtmpdir.
Anchor(write_view_matrix) write_view_matrix
Write the current view matrix to a file. Reads the file name from subjtmpdir.
Anchor(write_vrml) 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 align_sphere] [#do_lighting_model do_lighting_model] [#draw_cursor draw_cursor] [#left_click left_click] [#make_lateral_view make_lateral_view] [#move_window move_window] [#redraw redraw] [#rotate_brain_x rotate_brain_x] [#rotate_brain_y rotate_brain_y] [#rotate_brain_z rotate_brain_z] [#scale_brain scale_brain] [#send_current_labels send_current_labels] [#show_flat_regions show_flat_regions] [#translate_brain_x translate_brain_x] [#translate_brain_y translate_brain_y] [#translate_brain_z translate_brain_z] [#read_really_matrix read_really_matrix] [#read_view_matrix read_view_matrix] [#really_center_brain really_center_brain] [#really_rotate_brain_x really_rotate_brain_x] [#really_rotate_brain_y really_rotate_brain_y] [#really_rotate_brain_z really_rotate_brain_z] [#really_scale_brain really_scale_brain] [#really_translate_brain really_translate_brain] [#resize_brain resize_brain] [#resize_window resize_window] [#restore_zero_position restore_zero_position] [#restore_initial_position restore_initial_position] [#transform_brain transform_brain] [#write_view_matrix write_view_matrix] [#write_really_matrix write_really_matrix]
I/O
[#func_load_timecourse func_load_timecourse] [#func_load_timecourse_offset func_load_timecourse_offset] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_save labl_save] [#labl_save_all labl_save_all] [#read_annotations read_annotations] [#read_binary_curv read_binary_curv] [#read_binary_decimation read_binary_decimation] [#read_binary_dipoles read_binary_dipoles] [#read_binary_sulc read_binary_sulc] [#read_binary_surf read_binary_surf] [#read_binary_values read_binary_values] [#read_binary_values_frame read_binary_values_frame] [#read_binary_patch read_binary_patch] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_curv_to_val read_curv_to_val] [#read_fieldsign read_fieldsign] [#read_fsmask read_fsmask] [#read_imag_vals read_imag_vals] [#read_labeled_vertices read_labeled_vertices] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_write_dotw sclv_write_dotw] [#write_binary_curv write_binary_curv] [#write_binary_dipoles write_binary_dipoles] [#write_binary_patch write_binary_patch] [#write_binary_surface write_binary_surface] [#write_binary_sulc write_binary_sulc] [#write_fieldsign write_fieldsign] [#write_fsmask write_fsmask] [#write_labeled_vertices write_labeled_vertices] [#write_vrml write_vrml]
Curvature Operations
[#clear_curvature clear_curvature] [#compute_curvature compute_curvature] [#curv_to_val curv_to_val] [#fill_flood_from_cursor fill_flood_from_cursor] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#smooth_curv smooth_curv] [#val_to_curv val_to_curv]
Overlay Operations
[#curv_to_val curv_to_val] [#f_to_t f_to_t] [#fill_flood_from_cursor fill_flood_from_cursor] [#label_to_stat label_to_stat] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#sclv_copy_all_view_settings_from_current_field sclv_copy_all_view_settings_from_current_field] [#sclv_copy_view_settings_from_current_field sclv_copy_view_settings_from_current_field] [#sclv_copy_view_settings_from_field sclv_copy_view_settings_from_field] [#sclv_get_normalized_color_for_value sclv_get_normalized_color_for_value] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_send_current_field_info sclv_send_current_field_info] [#sclv_send_histogram sclv_send_histogram] [#sclv_set_current_field sclv_set_current_field] [#sclv_set_current_threshold_from_percentile sclv_set_current_threshold_from_percentile] [#sclv_set_current_threshold_using_fdr sclv_set_current_threshold_using_fdr] [#sclv_set_current_timepoint sclv_set_current_timepoint] [#sclv_set_overlay_alpha sclv_set_overlay_alpha] [#sclv_smooth sclv_smooth] [#sclv_write_dotw sclv_write_dotw] [#stat_to_val stat_to_val] [#swap_val_val2 swap_val_val2] [#val_to_curv val_to_curv] [#val_to_stat val_to_stat]
Vertex Operations
[#fill_flood_from_cursor fill_flood_from_cursor] [#find_orig_vertex_coordinates find_orig_vertex_coordinates] [#fix_nonzero_vals fix_nonzero_vals] [#flip_normals flip_normals] [#invert_face invert_face] [#invert_surface invert_surface] [#invert_vertex invert_vertex] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#set_current_vertex_set set_current_vertex_set] [#show_surf show_surf] [#shrink shrink] [#swap_vertex_fields swap_vertex_fields]
Cursor Operations
[#draw_cursor draw_cursor] [#resend_to_subject resend_to_subject] [#select_orig_vertex_coordinates select_orig_vertex_coordinates] [#select_talairach_point select_talairach_point] [#select_vertex_by_vno select_vertex_by_vno] [#send_spherical_point send_spherical_point] [#send_to_subject send_to_subject]
Ripping and Cutting Operations
[#clear_ripflags clear_ripflags] [#cut_line cut_line] [#cut_plane cut_plane] [#dilate_ripped dilate_ripped] [#restore_ripflags restore_ripflags] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] [#undo_last_action undo_last_action]
Reporting Information
[#dump_vertex dump_vertex] [#get_selected_path_vnos get_selected_path_vnos] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#plot_curv plot_curv]
Screen Shots
[#save_rgb save_rgb] [#save_rgb_cmp_frame save_rgb_cmp_frame] [#save_tiff save_tiff]
Marking Operations
[#clear_all_vertex_marks clear_all_vertex_marks] [#clear_vertex_marks clear_vertex_marks] [#close_marked_vertices close_marked_vertices] [#get_selected_path_vnos get_selected_path_vnos] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#mark_annotation mark_annotation] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#mark_face mark_face] [#mark_faces mark_faces] [#mark_vertex mark_vertex] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] [#val_to_mark val_to_mark]
Label Operations
[#label_to_stat label_to_stat] [#labl_dilate labl_dilate] [#labl_erode labl_erode] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#labl_remove labl_remove] [#labl_remove_all labl_remove_all] [#labl_save labl_save] [#labl_save_all labl_save_all] [#labl_select labl_select] [#labl_set_color labl_set_color] [#labl_set_info labl_set_info] [#labl_set_name_from_table labl_set_name_from_table] [#labl_select_label_by_vno labl_select_label_by_vno] [#mask_label mask_label] [#send_current_labels send_current_labels]
Time Courses
[#func_clear_selection func_clear_selection] [#func_graph_timecourse_selection func_graph_timecourse_selection] [#func_load_timecourse func_load_timecourse] [#func_load_timecourse_offset func_load_timecourse_offset] [#func_print_timecourse_selection func_print_timecourse_selection] [#func_select_label func_select_label] [#func_select_marked_vertices func_select_marked_vertices]
Paths
[#path_new_path_from_marked_vertices path_new_path_from_marked_vertices] [#path_remove_selected_path path_remove_selected_path] [#path_select path_select]
Unsupported Functions
Anchor(add_subject_to_average_curvim) add_subject_to_average_curvim subjectName morphSubdirectory
Anchor(clear_all_vertex_cursor) clear_all_vertex_cursor
Anchor(compute_angles) compute_angles
Anchor(compute_CMF) compute_CMF
Anchor(compute_cortical_thickness) compute_cortical_thickness
Anchor(compute_fieldsign) compute_fieldsign
Anchor(compute_pval_fwd) compute_pval_fwd pvalThreshold
pvalThreshold is a floating point number.
Anchor(compute_pval_inv) compute_pval_inv
Anchor(compute_select_fwd) compute_select_fwd maximumDistance
maximumDistance is a floating point number in millimeters.
Anchor(compute_timecourses) compute_timecourses
Anchor(curv_shrink_to_fill) curv_shrink_to_fill numberOfSteps
Anchor(curv_to_curvim) curv_to_curvim
Anchor(curvim_to_second_surface) curvim_to_second_surface
Anchor(curvim_to_surface) curvim_to_surface
Anchor(deconvolve_weights) deconvolve_weights weightFileName scaleFileName
Anchor(draw_all_cursor) draw_all_cursor
Anchor(draw_all_vertex_cursor) draw_all_vertex_cursor
Anchor(draw_curvature_line) draw_curvature_line
Anchor(draw_fundus) draw_fundus
Anchor(draw_radius) draw_radius
Anchor(draw_theta) draw_theta
Anchor(draw_vector) draw_vector fileName
Reads an x/y vector from fileName and draws it to the screen.
Anchor(ellipsoid_morph) ellipsoid_morph numberOfSteps rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
numberOfSteps is an integer. All distances are in millimeters and should be millimeters.
Anchor(ellipsoid_project) ellipsoid_project rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
- All distances are in millimeters and should be millimeters.
Anchor(ellipsoid_shrink) ellipsoid_shrink numberOfSteps radius
radius is in millimeters.
Anchor(ellipsoid_shrink_bug) ellipsoid_shrink_bug numberOfSteps radius length
radius and length is in millimeters.
Anchor(f_to_p) f_to_p DOFnumerator DOFdenominator
Anchor(flatten) flatten
Reads the file name from subjtmpdir.
Anchor(fill_second_surface) fill_second_surface
Anchor(filter_recs) filter_recs
Anchor(load_gcsa) load_gcsa fileName
Anchor(load_vals_from_sol) 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.
Anchor(load_var_from_sol) load_var_from_sol condition
condition is an integer.
Anchor(make_lateral_view_second) make_lateral_view_second
Anchor(normalize_area) normalize_area
Anchor(normalize_binary_curv) normalize_binary_curv
Anchor(normalize_inverse) normalize_inverse
Anchor(normalize_second_binary_curv) normalize_second_binary_curv
Anchor(normalize_time_courses) 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.
Anchor(open_window) open_window
Anchor(orient_sphere) orient_sphere
Anchor(plot_all_time_courses) plot_all_time_courses
Anchor(plot_marked) plot_marked fileName
Generates a summary file of data from all marked vertices in fileName.
Anchor(put_retinotopy_stats_in_vals) put_retinotopy_stats_in_vals
- Calculates retinotopy values at each vertex and stores them in the first overlay layer.
Anchor(read_and_color_labeled_vertices) 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.
Anchor(read_and_smooth_parcellation) 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.
Anchor(read_annotated_image) read_annotated_image
Will read the file from annot.
Anchor(read_curv_images) read_curv_images
- Loads files into the curvim array.
Anchor(read_disc) read_disc subjectName
Anchor(read_iop) read_iop fileName dipoleFileNumber
Anchor(read_ncov) read_ncov fileName
Anchor(read_parcellation) 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.
Anchor(read_plot_list) read_plot_list fileName
Anchor(read_rec) read_rec fileName
Anchor(read_second_binary_curv) read_second_binary_curv
Reads a curvature file into mris2. Reads the file name from targcurv.
Anchor(read_second_binary_surf) read_second_binary_surf
Reads mris2. Reads the file name from targsurf.
Anchor(read_soltimecourse) read_soltimecourse fileName
Anchor(read_stds) read_stds conditionNumber
- Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field.
Anchor(read_surf) read_surf fileName
- Reads only vertex positions from a file into the main surface, overwriting the original positions.
Anchor(read_vertex_list) read_vertex_list fileName
Anchor(really_align_brain) really_align_brain
- Aligns first surface to second.
Anchor(really_center_second_brain) really_center_second_brain
- Works on the second mris.
Anchor(redraw_second) redraw_second
- Draws second surface.
Anchor(remove_triangle_links) remove_triangle_links
Calls MRISremoveTriangleLinks.
Anchor(restore_surf) restore_surf
- Restores the vertex positions in the temp position to the main position.
Anchor(save_surf) save_surf
- Saves the vertex positions in the main position to the temp position.
Anchor(sclv_read_from_dotw_frame) sclv_read_from_dotw_frame
- This seems to load in a surface full of values, and then individual values, from a file.
Anchor(second_surface_curv_to_curvim) second_surface_curv_to_curvim
- Works on mris2.
Anchor(shift_values) shift_values
- Places the values from the first overlay field into the second.
Anchor(smooth_curvim) smooth_curvim numberOfSteps
Anchor(smooth_curvim_sparse) smooth_curvim_sparse numberOfSteps
Anchor(sphere_shrink) sphere_shrink numberOfSteps radius
radius is in millimeters.
Anchor(smooth_fs) smooth_fs numberOfSteps
Smooths the field sign values by numberOfSteps, an integer.
Anchor(smooth_val) smooth_val numberOfSteps
- sclv_smooth is used instead.
Anchor(smooth_val_sparse) smooth_val_sparse numberOfSteps
Anchor(sol_plot) sol_plot timePoint plotType
Uses the dlat value in computing the range.
Anchor(subsample_dist) subsample_dist spacing
Used in decimation. Calls MRISsubsampleDist. spacing is an integer.
Anchor(subsample_orient) subsample_orient spacing
Used in decimation. spacing is an integer.
Anchor(swap_buffers) swap_buffers
Anchor(swap_curv) swap_curv
- Swaps the curv and curvbak fields.
Anchor(swap_stat_val) swap_stat_val
- Swaps the values in the first overlay field and the fifth.
Anchor(swap_val_val2) swap_val_val2
- Swaps the values in the first overlay field and the second.
Anchor(swap_values) swap_values
- Swaps the values in the first overlay field and the second.
Anchor(t_to_p) t_to_p DOF
Anchor(to_double_buffer) to_double_buffer
Anchor(to_single_buffer) to_single_buffer
Anchor(twocond) twocond condition condition
- Both conditions are integers.
Anchor(write_binary_areas) write_binary_areas
Calls MRISwriteArea. Will read the file name from area.
Anchor(write_binary_decimation) write_binary_decimation
Calls MRISwriteDecimation. Will read the file name from dec.
Anchor(write_binary_values) write_binary_values
Calls MRISwriteValues. Will read the file name from val.
Anchor(write_curv_images) write_curv_images
Will read the file name from targcurvim.
Anchor(write_decimation) write_decimation
Will read the file name from dec.
Anchor(write_dipoles) write_dipoles
Will read the file name from dip.
Anchor(write_fill_images) write_fill_images
Anchor(write_subsample) write_subsample
Writes an ASCII file. Will read the file name from fs.
Index
[#add_subject_to_average_curvim add_subject_to_average_curvim] [#clear_all_vertex_cursor clear_all_vertex_cursor] [#compute_angles compute_angles] [#compute_CMF compute_CMF] [#compute_cortical_thickness compute_cortical_thickness] [#compute_fieldsign compute_fieldsign] [#compute_pval_fwd compute_pval_fwd] [#compute_pval_inv compute_pval_inv] [#compute_select_fwd compute_select_fwd] [#compute_timecourses compute_timecourses] [#curv_shrink_to_fill curv_shrink_to_fill] [#curv_to_curvim curv_to_curvim] [#curvim_to_second_surface curvim_to_second_surface] [#curvim_to_surface curvim_to_surface] [#deconvolve_weights deconvolve_weights] [#draw_all_cursor draw_all_cursor] [#draw_all_vertex_cursor draw_all_vertex_cursor] [#draw_curvature_line draw_curvature_line] [#draw_fundus draw_fundus] [#draw_radius draw_radius] [#draw_theta draw_theta] [#draw_vector draw_vector] [#ellipsoid_morph ellipsoid_morph] [#ellipsoid_project ellipsoid_project] [#ellipsoid_shrink ellipsoid_shrink] [#ellipsoid_shrink_bug ellipsoid_shrink_bug] [#f_to_p f_to_p] [#flatten flatten] [#fill_second_surface fill_second_surface] [#filter_recs filter_recs] [#load_gcsa load_gcsa] [#load_vals_from_sol load_vals_from_sol] [#load_var_from_sol load_var_from_sol] [#make_lateral_view_second make_lateral_view_second] [#normalize_area normalize_area] [#normalize_binary_curv normalize_binary_curv] [#normalize_inverse normalize_inverse] [#normalize_second_binary_curv normalize_second_binary_curv] [#normalize_time_courses normalize_time_courses] [#open_window open_window] [#orient_sphere orient_sphere] [#plot_all_time_courses plot_all_time_courses] [#plot_marked plot_marked] [#put_retinotopy_stats_in_vals put_retinotopy_stats_in_vals] [#read_and_color_labeled_vertices read_and_color_labeled_vertices] [#read_and_smooth_parcellation read_and_smooth_parcellation] [#read_annotated_image read_annotated_image] [#read_curv_images read_curv_images] [#read_disc read_disc] [#read_iop read_iop] [#read_ncov read_ncov] [#read_parcellation read_parcellation] [#read_plot_list read_plot_list] [#read_rec read_rec] [#read_second_binary_surf read_second_binary_surf] [#read_second_binary_curv read_second_binary_curv] [#read_soltimecourse read_soltimecourse] [#read_stds read_stds] [#read_surf read_surf] [#read_vertex_list read_vertex_list] [#really_align_brain really_align_brain] [#really_center_second_brain really_center_second_brain] [#redraw_second redraw_second] [#remove_triangle_links remove_triangle_links] [#restore_surf restore_surf] [#save_surf save_surf] [#sclv_read_from_dotw_frame sclv_read_from_dotw_frame] [#second_surface_curv_to_curvim second_surface_curv_to_curvim] [#shift_values shift_values] [#smooth_curvim smooth_curvim] [#smooth_curvim_sparse smooth_curvim_sparse] [#sphere_shrink sphere_shrink] [#smooth_fs smooth_fs] [#smooth_val smooth_val] [#smooth_val_sparse smooth_val_sparse] [#sol_plot sol_plot] [#subsample_dist subsample_dist] [#subsample_orient subsample_orient] [#swap_buffers swap_buffers] [#swap_curv swap_curv] [#swap_stat_val swap_stat_val] [#swap_stat_val2 swap_stat_val2] [#swap_values swap_values] [#t_to_p t_to_p] [#to_single_buffer to_single_buffer] [#to_double_buffer to_double_buffer] [#twocond twocond] [#write_binary_areas write_binary_areas] [#write_binary_decimation write_binary_decimation] [#write_binary_values write_binary_values] [#write_curv_images write_curv_images] [#write_decimation write_decimation] [#write_dipoles write_dipoles] [#write_fill_images write_fill_images] [#write_subsample write_subsample]