.. _KeyboardControls: Keyboard Controls ----------------- *On MACs*, Alt is the Apple/Command key. If it is commandeered by the OS, and you can't get it back, then try the alt/option key instead. *On Linux*, Turn NumLock OFF, otherwise certain mouse or keyboard combinations do not work as intended. .. _LC_a: :ref:`a `: attenuation by background, toggle. See also :ref:`Plane Layering` .. _UC_B: :ref:`B `: Backface/Frontface/Noface culling, toggle. .. _LC_b: :ref:`b `: background color, toggle. See also :ref:`Plane Layering ` .. _LC_c: :ref:`c `: load a node color file. .. _LC_Ctrl+d: :ref:`Ctrl+d `: Open draw :ref:`ROI controller`, and put cursor in drawing mode. .. _UC_D: :ref:`D `: Attch to the current dataset 'parent' a dot product transform. The 'child' (transformed) dataset is created by calculating the dot product between each node time series and the time series of the current node. Each time you 'shift+ctrl+click (drag too if you like)' on the surface, with the child dataset in view, the dot product is recalculated. You can save the resultant datasets with 'ctrl+W' key (see below). Dset names are automatically formed. To stop the interactive dot product computations, switch back to the parent dset and press 'D' again. If the parent dataset is properly detrended and each time series is normalized so that its stdev is 1.0 then the dot product is the cross correlation coefficient. Detrending and normalization can be carried out with: 3dDetrend -polort 4 -normalize \ -prefix dt.TS.niml.dset \ v2s.TS.niml.dset You can get a good feel for what this 'D' does by running @Install_InstaCorr_Demo That script will download and setup demo data for resting-state correlations. In particular, script @RunSingleSurfInstaCorr of the demo illustrates the 'D' feature. .. _UC_F: :ref:`F `: Flip light position between +z and -z. .. _LC_f: :ref:`f `: functional overlay, toggle. .. _LC_g: :ref:`g `: graph data. Open a graphing window for the dataset currently selected. The graphing window updates with each new node selection. A graphing window can be opened for each dataset, and all graphs will update unless '1 Only' is set in Surface Controller. For complex data its magnitude is plotted instead. Use 'ctrl+h' in graph window for more help. .. _UC_H: :ref:`H `: Highlight nodes inside a specified box. Does not update other viewers Paints into existing colors Highlight is wiped out with new colors. .. _LC_Ctrl+h: :ref:`Ctrl+h `: help message .. _UC_J: :ref:`J `: Set the selected FaceSet on Surface Object in Focus. Does not update in other viewers or in AFNI. .. _LC_j: :ref:`j `: Set the cross hair to a certain node on SO in Focus. Append/prepend L or R to switch hemispheres. Does update in other viewers if linked by index and AFNI if connected .. _LC_Ctrl+j: :ref:`Ctrl+j `: Set the cross hair's XYZ location. Does update in other viewers if linked by XYZ and AFNI if connected .. _LC_Alt+j: :ref:`Alt+j `: Set the Focus node. Cross hair's XYZ remain unchanged. Does not update in other viewers or in AFNI .. _UC_L: :ref:`L `: Light's XYZ coordinates. Default setting is 0.0 0.0 1.0 .. _UC_Ctrl+L: :ref:`Ctrl+L `: Brighten specular and diffuse lights by a factor of 1/0.8 .. _LC_l: :ref:`l `: look at point .. _LC_Alt+l: :ref:`Alt+l `: look at cross hair .. _LC_Ctrl+l: :ref:`Ctrl+l `: Dim specular and diffuse lights by a factor of 0.8 .. _UC_Alt+Ctrl+M: :ref:`Alt+Ctrl+M `: Dumps memory trace to file called malldump.NNN where NNN is the smallest number between 001 and 999 that has not been used. .. _LC_m: :ref:`m `: momentum, toggle .. _UC_O: :ref:`O `: Increase opacity of all surfaces in viewer by 4 levels. Transparency levels accessible are: 0 (opaque), 25%, 50%, 75%, 100% (invisible) .. _UC_Ctrl+O: :ref:`Ctrl+O `: Increase opacity of selected object by 4 levels. .. _LC_o: :ref:`o `: Decrease opacity of all surfaces in viewer by 4 levels. .. _LC_Ctrl+o: :ref:`Ctrl+o `: Decrease opacity of selected object by 4 levels. .. _LC_Alt+o: :ref:`Alt+o `: Set new center of rotation. Enter nothing to go back to default. .. _LC_Ctrl+n: :ref:`Ctrl+n `: Open a new surface viewer window. .. _LC_p: :ref:`p `: Viewer rendering mode (Fill, Line, Points, Hide), switch. .. _LC_Ctrl+p: :ref:`Ctrl+p `: Selected object rendering mode (Fill, Line, Points, Hide), switch. .. _LC_Alt+p: :ref:`Alt+p `: Cycle between restrictions of where DO node-based objects are displayed. Available modes are: All: No restrictions n3Crosshair: Crosshair node + 3 neighboring layers n2Crosshair: Crosshair node + 2 neighboring layers n1Crosshair: Crosshair node only None: Show nothing. See also -do_draw_mask option in DriveSuma ** DO stands for displayable objects, see also :ref:`Ctrl+Alt+s` below. ** For the moment, 'Alt+p' only applies to segment and sphere DOs that are node based. If you need it applied to other DOs, let me know. .. _UC_P: :ref:`P `: Reset viewer and all surfaces to Fill rendering mode. .. _LC_r: :ref:`r `: record current image in an a la AFNI image viewer. Identical images are rejected. If you just save one image, the recording window has no visible controls for saving the image. Either take another picture, or use 'Shift+right click' to get a menu. .. _LC_Ctrl+r: :ref:`Ctrl+r `: Record current image directly to disk. Images are saved with a date stamp of the format PREFIX.X.yymmdd_hhmmss.MMM.jpg where: PREFIX controlled with SUMA_AutoRecordPrefix. See environment variable SUMA_AutoRecordPrefix for controlling prefix and output image type (suma -update_env). X The character indicating which viewer is recording (you can record from multiple viewers at once. yy, mm, dd, hh, mm, ss for year, month, day, hours, minutes, and seconds, respectively. MMM is a millisecond marker to avoid overwriting files. Unlike the other recording mode (with the 'R' key), there is no rejection of identical images This option is useful for saving a large number of images without running out of memory in the recorder GUI. Your current PREFIX is: ./SUMA_Recordings/autorecord.jpg .. _LC_Alt+r: :ref:`Alt+r `: Increase the image oversampling factor. By increasing this factor, you can create images at a resolution higher than that of the SUMA window. This is done by subdividing the scene into NxN sections and rendering each section separately. The NxN renderings are saved in the image recorder. After you save the images to disk, you can stitch them using imcat (a la AFNI montage). Note that each section is still rendered at the resolution of the SUMA window. So the bigger the window the more resolution per section. However, you cannot exceed a certain limit on the number of pixels in the final image. This limitation is due to the graphics card on your system. SUMA will take care not to exceed this limit. .. _UC_Ctrl+R: :ref:`Ctrl+R `: Toggle continuous jpeg saving to disk. Naming of output images is automatic, same as in Ctrl+r. See help for Ctrl+r above for more info. .. _UC_R: :ref:`R `: Toggle continuous recording to an a la AFNI image viewer. Identical images are rejected. .. _LC_Ctrl+s: :ref:`Ctrl+s `: Open :ref:`controller ` for surface in Focus. .. _load_DOs: .. _LC_Ctrl+Alt+s: :ref:`Ctrl+Alt+s `: Input filename containing displayable objects (a.k.a. :ref:`DOs`). Files are of 1D format with a necessary comment at the top to indicate the type of objects in the file. Note 1: Repeatedly loading files with the same name will replace currently loaded versions. Note 2: Node-based (Types 3 and 4) objects will follow a node when its coordinates change. Note 3: See also 'Alt+p' for restricting which node-based objects get displayed. .. _load_segments: Type 1: :ref:`Segments` between (x0,y0,z0) and (x1,y1,z1) 1st line must be '#segments' (without quotes), or '#oriented_segments' (slower to render). One can also use #node-based_segments or #node-based_oriented_segments and use a node index in place of (x,y,z) triplets. Remainder of file is N rows, each defining a segment (or a vector) between two points. Column content depends on the number of columns in the file: For node-based: 2 cols: n0 n1 3 cols: n0 n1 th with th being line thickness 6 cols: n0 n1 c0 c1 c2 c3 with c0..3 being the RGBA values between 0 and 1.0 7 cols: n0 n1 c0 c1 c2 c3 th 8 cols: n0 n1 c0 c1 c2 c3 th st with st being a stippling, or dashing for some, flag. Use integers between 1 and 5 for a variety of syles. For coordinate-based 6 cols: x0 y0 z0 x1 y1 z1 7 cols: x0 y0 z0 x1 y1 z1 th with th being line thickness 10 cols: x0 y0 z0 x1 y1 z1 c0 c1 c2 c3 with c0..3 being the RGBA values between 0 and 1.0 11 cols: x0 y0 z0 x1 y1 z1 c0 c1 c2 c3 th 12 cols: x0 y0 z0 x1 y1 z1 c0 c1 c2 c3 th st with st defined above. .. _load_directions: Type 2: :ref:`Directions`, a variant of segments and oriented segments. 1st line must be '#directions' (without quotes). Remainder of file is N rows, each defining a direction. Column content depends on the number of columns in the file: 3 cols: dx dy dz with dx dy dz defining the direction. The triplet need not be of unti norm though that would affect the default coloring scheme detailed below. The segment drawn has origin 0, 0, 0 4 cols: dx dy dz mag with mag being a scaling factor for the direction. mag is 1 by default. 5 cols: dx dy dz mag th with th being the thickness of the line. Default is 1 6 cols: ox oy oz dx dy dz Specify the origin of the segment in o1, o2, o3. Default is origin 0, 0, 0 for all 7 cols: o1 o2 o3 dx dy dz mag Add individual scaling factors to case above Segment is from origin to origin+mag*direction 8 cols: o1 o2 o3 dx dy dz mag th Add thickness to case with 7 columns 9 cols: dx dy dz mag th c0 c1 c2 c3 Add colors for each segment, with origin at 0,0,0 11 cols: ox oy oz dx dy dz mag c0 c1 c2 c3 12 cols: ox oy oz dx dy dz mag th c0 c1 c2 c3 .. _load_spheres: Type 3: :ref:`Spheres` centered at (ox, oy, oz) 1st line must be '#spheres' (without quotes). Remainder of file is N rows, each defining a sphere. Column content depends on the number of columns in the file: 3 cols: ox oy oz 4 cols: ox oy oz rd with rd being the radius of the sphere 5 cols: ox oy oz rd st with st being the style of the sphere's rendering. Choose from: 0: points 1: Lines 2: Filled 7 cols: ox oy oz c0 c1 c2 c3 with c0..3 being the RGBA values between 0 and 1.0 8 cols: ox oy oz c0 c1 c2 c3 rd 9 cols: ox oy oz c0 c1 c2 c3 rd st .. _load_points: Type 4: :ref:`Points` at (ox, oy, oz) 1st line must be '#points' (without quotes). Remainder of file is N rows, each defining a point. Column content depends on the number of columns in the file: 3 cols: ox oy oz 4 cols: ox oy oz sz with sz being the size of the point 7 cols: ox oy oz c0 c1 c2 c3 with c0..3 being the RGBA values between 0 and 1.0 8 cols: ox oy oz c0 c1 c2 c3 sz .. _load_node-based_vectors: Type 5: :ref:`Vectors` (vx, vy, vz) at surface nodes 1st line must be '#node-based_vectors' (without quotes) or '#node-based_ball-vectors' (slower to render). Remainder of file is N rows, each defining a a vector at a particular node of the current surface. Column content depends on the number of columns in the file: 3 cols: vx, vy, vz node index 'n' is implicit equal to row index. Vector 'v' is from coordinates of node 'n' to coordinates of node 'n' + 'v' 4 cols: n, vx, vy, vz Here the node index 'n' is explicit. You can have multiple vectors per node, one on each row. 5 cols: n, vx, vy, vz, gn with gn being a vector gain factor 8 cols: n, vx, vy, vz, c0 c1 c2 c3 with with c0..3 being the RGBA values between 0 and 1.0 9 cols: n, vx, vy, vz, c0 c1 c2 c3 gn .. _load_node-based_spheres: Type 6: :ref:`Spheres` centered at nodes n of the current surface 1st line must be '#node-based_spheres' (without quotes). Remainder of file is N rows, each defining a sphere. Column content depends on the number of columns in the file, see Type 2 for more details: 1 cols: n 2 cols: n rd 3 cols: n rd st 5 cols: n c0 c1 c2 c3 6 cols: n c0 c1 c2 c3 rd 7 cols: n c0 c1 c2 c3 rd st .. _load_planes: Type 7: :ref:`Planes` defined with: ax + by + cz + d = 0. 1st line must be '#planes' (without quotes). Remainder of file is N rows, each defining a plane. Column content depends on the number of columns in the file: 7 cols: a b c d cx cy cz with the plane's equation being: ax + by + cz + d = 0 cx,cy,cz is the center of the plane's representation. Yes, d is not of much use here. There are no node-based planes at the moment. They are a little inefficient to reproduce with each redraw. Complain if you need them. .. _load_nido: Type 8: :ref:`Another` class of displayble objects is described in the output of :ref:`suma -help_nido` and the demonstration script :ref:`@DO.examples<@DO.examples>`. This new class allows for displaying text and figures in both screen and world space. .. _LC_Alt+s: :ref:`Alt+s `: Switch mouse buttons 1 and 3. .. _LC_t: :ref:`t `: talk to AFNI, toggle. .. _LC_Ctrl+t: :ref:`Ctrl+t `: Force a resend of surfaces to AFNI. .. _UC_T: :ref:`T `: Start listening for niml connections .. _LC_Ctrl+u: :ref:`Ctrl+u `: Open SUMA controller. .. _LC_w: :ref:`w `: Whereami window of little use at the moment. .. _UC_Ctrl+W: :ref:`Ctrl+W `: Write items stowed in SUMA's save list. This is used to write temporary dsets that are created on the fly in SUMA. Such sets include those created via the 'D' option above, or the results sent by 3dGroupInCorr .. _UC_W: :ref:`W `: Write ascii files containing the NodeList, the FaceSetList and the nodecolors of the surface in focus. .. _UC_Z: :ref:`Z `: Zoom in .. _LC_z: :ref:`z `: Zoom out .. _LC_[: :ref:`[ `: Show/Hide left hemisphere. .. _LC_]: :ref:`] `: Show/Hide right hemisphere. Window title shows which hemispheres are shown :-RL-: or :--: .. _LC_8: :ref:`8 `: Set the number of smoothing iterations to be applied to the foreground colors. This setting will be applied to all subsequent color sets. .. _LC_*: :ref:`* `: Smooth node colors by averaging with neighbors. The smoothing is only applied to the current colors, and will be not be applied to new color sets. .. _LC_,: :ref:`, ` .. _LC_.: :ref:`. ` (think ): Switch to next/previous view state. Viewing angle is reset only when switching to a state with flat surfaces. See :term:`state` for more on the meaning of states for different object types. .. _SPACE: :ref:`SPACE `: Toggle between Mapping Reference and Current view state. Viewing angle is reset only when switching to a state with flat surfaces. .. _L-R_arrows: :ref:`L-R arrows `: rotate about screen's Y axis .. _U-D_arrows: :ref:`U-D arrows `: rotate about screen's X axis .. _Shift+L-R_arrows: :ref:`Shift+L-R arrows `: translate along screen's X axis .. _Shift+U-D_arrows: :ref:`Shift+U-D arrows ` arrows: translate along screen's Y axis .. _Ctrl+L-R_arrows: :ref:`Ctrl+L-R arrows `: LR cardinal views .. _Ctrl+U-D_arrows: :ref:`Ctrl+U-D arrows `: IS cardinal views .. _Ctrl+Shift+U-D_arrows: :ref:`Ctrl+Shift+U-D arrows `: AP cardinal views .. _Ctrl+Shift+L-R_arrows: :ref:`Ctrl+Shift+L-R arrows `: rotate CCW and CW about Z screen axis .. _Alt+L-R_arrows: :ref:`Alt+L-R arrows `: Move selected node to neighboring nodes in the direction of the screen's X axis. The default is to move one node at a time. You can alter this setting with the environment variable: SUMA_KeyNodeJump in your ~/.sumarc file. .. _Alt+U-D_arrows: :ref:`Alt+U-D arrows `: Same as Alt+L-R but in the direction of the screen's Y axis .. _F1: :ref:`F1 `: screen axis (X-Red, Y-Green), toggle. .. _F2: :ref:`F2 `: surface axis (X-Red, Y-Green, Z-Blue), switch. .. _F3: :ref:`F3 `: cross hair, toggle. .. _F4: :ref:`F4 `: node/voxel/edge/cell/tract/tie selection highlight, toggle. .. _F5: :ref:`F5 `: FaceSet/Slice selection highlight, toggle. .. _F6: :ref:`F6 `: Viewer background color, toggle. .. _F7: :ref:`F7 `: Switch between color mixing modes. ORIG: Col = ( 1 - opacity ) * OldCol + opacity * NewCol MOD1: Col = ( 1 - opacity ) * OldCol + NewCol .. _F8: :ref:`F8 `: Viewing mode (Perspective or Orthographic Projection), toggle. .. _F9: :ref:`F9 `: Labels at cross hair, toggle. .. _F10: :ref:`F10 `: Toggle prying axis between surfaces' Z and Y axes. .. _F11: :ref:`F11 `: Change object rendering order. This order will affect the resultant image in the few instances where alpha transparency is used. The order can be specified for only three types of objects for now: graphs, surfaces, and volumes. If you want to render graphs first, followed by volumes then surfaces then set SUMA_ObjectDisplayOrder to something like: 'graph,vol,surf', or 'GVS' .. _F12: :ref:`F12 `: Time 20 scene renderings. .. _HOME: :ref:`HOME `: reset zoom and recenter surfaces. rest view angle for flat surfaces only. .. _ESCAPE: :ref:`ESCAPE `: close the surface viewer window. .. _Shift+ESCAPE: :ref:`Shift+ESCAPE `: close all surface viewer windows. .. _MouseControls: Mouse Controls -------------- *On MACs*, Alt is the Apple/Command key. If it is commandeered by the OS, and you can't get it back, then try the alt/option key instead. *On Linux*, Turn NumLock OFF, otherwise certain mouse or keyboard combinations do not work as intended. .. _Button_1-Motion: :ref:`Button 1-Motion `: For 3D scenes, rotation as if you were using a trackball. For matrix displays, Button 1-Motion causes translation because rotations are of little use in matrix display mode. Pure vertical motion is equivalent to using the up/down arrow keys. Pure horizontal motion is equivalent to using the left/right arrow keys. Of course, the advantage to using the mouse is a continuous range of rotation angles and simultaneous rotations about the screen's X & Y axis. .. _Shift+Button_1-Motion: :ref:`Shift+Button 1-Motion `: Rotate surfaces about the Z axis. This is useful at times for reorienting flat maps. .. _Shift+Button_1-DoubleClick: :ref:`Shift+Button 1-DoubleClick `: Undo Z rotation .. _Ctrl+Button_1-Motion: :ref:`Ctrl+Button 1-Motion `: Pry open two hemispheres so that you can see medial or lateral walls better from one angle. Prying is disabled for flat surfaces and with spheres the effect is to rotate each sphere about the Y axis passing through its center. Also, prying is only enabled when the state you are viewing contains two surfaces, one on the left and one on the right. in 3D views, left right mouse movement cause a rotation about the front or rear I/S axis. Up down movements cause a shift along the left/right direction. You can select nodes (Button 3) on pried surfaces and still have AFNI jump to the proper location, and vice versa. However for the moment, you cannot draw in pried mode. If you attempt to draw, the surfaces are put back together. To make best use of this option, you want to have env. variable SUMA_LHunify = YES (see your ~/.sumarc for help) .. _Button_1-DoubleClick: :ref:`Button 1-DoubleClick `: Reset to Home vieweing angle, zooming is left unchanged. See also 'HOME' key .. _Ctrl+Button_1-DoubleClick: :ref:`Ctrl+Button 1-DoubleClick `: Undo surface prying. .. _Button_2-Motion: :ref:`Button 2-Motion `: Translation for 3D scenes. Rotation for matrix displays. .. _Shift+Button2-Motion: :ref:`Shift+Button2-Motion ` or :kbd:`Button 1+2-Motion`: Zoom in/out .. _Button_3-Press: :ref:`Button 3-Press `: Node/Voxel/Edge/etc. picking. In ROI mode, initiates a path to new node in DrawROI mode. Picking of graph edges/nodes can get difficut when surfaces are also displayed. To help with that, see Alt+Button 3-Press next. Also see :ref:`Selecting Objects` below. .. _Alt+Button_3-Press: :ref:`Alt+Button 3-Press `: Graph edge/node picking in the presence of surfaces. Intersections with surfaces are ignored. .. _Shift+Alt+Button_3-Press: :ref:`Shift+Alt+Button 3-Press `: Same as Alt+Button 3, but also display pick buffer. This is mostly for debugging or for understanding why selection is behaving strangely. .. _Shift+Button_3-Press: :ref:`Shift+Button 3-Press `: Shows an image of the selection buffer for debugging purposes. In :ref:`Draw ROI Mode `, the selection buffer is not displayed and the effect of the click is to select a node, but not to include it in the ROI. .. _Ctrl+Button_3-Press: :ref:`Ctrl+Button 3-Press `: Yoke intensity selection to index of selected node*K. This is only possible if the currently visualized dataset has K times many sub-bricks as the surface has nodes. K is an integer. .. _Shift+Ctrl+Button_3-Press: :ref:`Shift+Ctrl+Button 3-Press `: Pick and initiate call in Dot xform mode, or to GroupInCorr .. _Button_3-DoubleClick: :ref:`Button 3-DoubleClick `: If double clicking on a tract mask, select the tract mask and turn the viewer into Mask Manipulation Mode. In this mode, the mask is shown as a wiremesh, and selections on any object will move the mask to that location. New tract/masks intersections are computed at the new location. To leave Mask Manipulation Mode, double click with button 3 either on the mask or in an area void of any objects. If double clicking with a graph object in focus and only connections from one node are shown, then revert to showing all graph connections. Without this, you can loose all other clickables if a certain node is not connected to anything. .. _Button_3-Motion: :ref:`Button 3-Motion `: continuous picking whenever surface are present. No calls for dot product (InstaCorr) or GroupInCorr, while dragging. Continuous picking of graph edges/nodes if no surfaces are displayed. See :ref:`Continuous Selection` below .. _Alt+Button_3-Motion: :ref:`Alt+Button 3-Motion `: Continuous picking of graph edges/nodes. Intersections with surfaces are ignored. .. _Ctrl+Button_3-Motion: :ref:`Ctrl+Button 3-Motion `: continous yoking of intensity selection to selected node*K. .. _Shift+Ctrl+Button_3-Motion: :ref:`Shift+Ctrl+Button 3-Motion `: Continuous picking and calls for dot product (InstaCorr) or GroupInCorr, while dragging. .. _Scroll: :ref:`Scroll ` or Wheel: Zoom in/out .. _Shift+Scroll: :ref:`Shift+Scroll ` or Shift+Wheel: change selected slice if current selected object is a volume. .. _Ctrl+Scroll: :ref:`Ctrl+Scroll ` or Ctrl+Wheel: change the size of the currently selected tract mask. This only works when you're in :ref:`mask manipulation mode`. .. _Selecting_Objects: Selecting Objects ----------------- Selections are done with the :ref:`right-mouse click ` unless you request :ref:`otherwise `. The selection of an object triggers a multitude of actions: * When :ref:`talking` to AFNI, a selection prompts AFNI to also jump to the corresponding location. SUMA can also talk to other programs such asHalloSuma * The controller for that object is popped to the top of the stack in the controllers notebook, and the crosshair information in the controller gets updated. * Other open SUMA controllers are made to jump to the corresponding locations. Use the SUMA controller (:ref:`Ctrl+u`) to setup how different controllers are locked together. * When in :ref:`drawing ROIs mode` a selection adds to the ROI being drawn. See :ref:`drawing_ROIs` for details, assuming it is written by now! * If you have 'click callbacks' initiated, a selection combined with the proper keyboard modifiers initiates a callback. An example of this would be the :ref:`surface-based instacorr` or the variety of instacorr features in AFNI and/or 3dGroupInCorr. The following command can download and install demo material for InstaCorr excitement:: @Install_InstaCorr_Demo -mini * If you are in :ref:`Mask Manipulation Mode` Selections will make the tract mask jump to the selection location. Picking behavior depends on the object being selected as follows: 1- Node picking on surfaces: Selection of a node on the surface involves finding intersected triangles, identifying the closest intersected triangle, and then indentifying the closest node within it. The crosshair is centered at the location of intersection and marked with a yellow sphere. The closest node in the triangle is marked with a small (tiny some say) blue sphere, and the triangle is highlighted with a gray line contour. Highlighting can be toggled with :ref:`F3 for crosshair`, :ref:`F4 for selected node`, and :ref:`F5 for the triangle` .. figure:: media/surface_selection.jpg :figwidth: 30% :align: center :name: media/surface_selection.jpg :ref:`(link)` 2- Voxel picking in volumes: You can select voxels on rendered slices as long as the voxels are not thresholded out of view. They maybe too dark to see but still be selectable if their value exceeds that of the threshold. Selecting a voxel also highlights the slice. You can turn off the highlight rectangle with :ref:`F5 `. Note that you can also select from the 3D rendered volume and when 3D rendering is turned on. In that case, no slice highlighting is done. 3- Edge/cell selection in graphs: Right click on an edge, matrix cell, or bundle reprenting the edge and the connection is rendered white. Because the graphs can be bidirectional, clicking on an edge between [n1, n2] with the click location closest to n1 would select edge n1-->n2, while clicking closer to n2 gets you edge n2-->n1. This also happens when you click on a bundle representation of the edge. The selected connection is highlighted in white and the highlighting can be toggled with the :ref:`F4 ` Selecting an edge on the 3D graph is reflected on the dual representation in matrix form by highlighting the equivalent cell, and vice versa. Selecting a node on the 3D graph, by clicking on the ball representing the node, or the node's name highlights only the connections to that node. The same type of selection can be made by clicking on a row or column's label in the matrix representation form. When graphs are represented along with volumes and surfaces, picking an edge can get tricky. In that case, use :ref:`Alt+Button 3` instead. 4- Tract selection: Right click on a tract - the hairline - for selecting a location along the tract. What's more to say ? .. _Continuous_Selection: Continuous Selection ^^^^^^^^^^^^^^^^^^^^ You can select and drag and sweep through numerous locations. The main thing to keep in mind is that when you have a multitute of object types, such as tracts, voxels, surfaces, etc. SUMA locks the selection to the object type selected at the beginning of the sweep. So, if you begin the selection on a surface and drag, then the selections during the sweep are restricted to surfaces only. .. _Viewer_Menus: Viewer Menus ------------ .. _File_Menu: File ^^^^ .. _Save_View: :ref:`Save View `: Save viewer's display settings. .. _Load_View: :ref:`Load View `: Load and apply display settings. .. _Close: :ref:`Close `: Close this viewer. Exit SUMA if this is the only viewer. .. _View_Menu: View ^^^^ .. _SUMA_Controller: :ref:`SUMA Controller `: Open SUMA controller interface. .. _Surface_Controller: :ref:`Surface Controller `: Open selected surface's controller interface. .. _Viewer_Controller: :ref:`Viewer Controller `: Open viewer's controller interface. .. _Cross_Hair: :ref:`Cross Hair `: Toggle cross hair display. .. _Node_in_Focus: :ref:`Node in Focus `: Toggle highlight of selected node. .. _Selected_Faceset: :ref:`Selected Faceset `: Toggle highlight of selected faceset. .. _Tools_Menu: Tools ^^^^^ .. _Draw_ROI: :ref:`Draw ROI `: Open :ref:`Draw ROI controller`, also with :ref:`Ctrl+d`. .. _Help_Menu: Help ^^^^ .. _Usage: :ref:`Usage `: Opens window with this message. .. _Message_Log: :ref:`Message Log `: Opens window that will contain errors and warnings typically output to screen. .. _SUMA_Global: :ref:`SUMA Global `: Output debugging information about some of SUMA's global structure's variables. .. _Viewer_Struct: :ref:`Viewer Struct `: Output debugging info on a viewer's structure. .. _Surface_Struct: :ref:`Surface Struct `: Output debugging info on the selected surface's struct. .. _InOut_Notify: :ref:`InOut Notify `: Turn on/off function in/out tracing. .. _MemTrace: :ref:`MemTrace `: Turn on memory tracing. Once turned on, this can't be turned off. .. _ENV_List: SUMA's env. ----------- Below is a list of all of SUMA's environment variables and their default values. You can query the value of a variable as SUMA sees it with: :command:`suma -Vname=` with 'name' replaced by the environment variable's name. e.gcommand:`suma -VSUMA_ArrowRotAngle=` *Always* update your environment variable list with: :command:`suma -update_env` List of Variables ^^^^^^^^^^^^^^^^^ .. _SUMA_ArrowRotAngle: :ref:`SUMA_ArrowRotAngle (env)`: Incremental arrow rotation angle in degrees default value: SUMA_ArrowRotAngle = 5 .. _SUMA_ColorPattern: :ref:`SUMA_ColorPattern (env)`: Color pattern (AFNI, EURO, PRINT, DEFAULT) default value: SUMA_ColorPattern = EURO .. _SUMA_SwapButtons_1_3: :ref:`SUMA_SwapButtons_1_3 (env)`: Swap mouse buttons 1 and 3 default value: SUMA_SwapButtons_1_3 = NO .. _SUMA_BackgroundColor: :ref:`SUMA_BackgroundColor (env)`: Background color r g b. No space between values default value: SUMA_BackgroundColor = 0.0,0.0,0.0 .. _SUMA_ROIColorMap: :ref:`SUMA_ROIColorMap (env)`: ROI color map (bgyr64, roi64, roi128, roi256) default value: SUMA_ROIColorMap = ROI_i256 .. _SUMA_NumConvSmooth: :ref:`SUMA_NumConvSmooth (env)`: Number of smoothing operations to run on convexity data default value: SUMA_NumConvSmooth = 5 .. _SUMA_ConvColorMap: :ref:`SUMA_ConvColorMap (env)`: Colormap for convexity (gray02, gray_i02, ngray20, bgyr64, etc.) default value: SUMA_ConvColorMap = gray02 .. _SUMA_ConvBrightFactor: :ref:`SUMA_ConvBrightFactor (env)`: Brightness factor for convexity default value: SUMA_ConvBrightFactor = 0.5 .. _SUMA_NumForeSmoothing: :ref:`SUMA_NumForeSmoothing (env)`: Number of smoothing operations to run on mixed foregroung color plane before mixing with background default value: SUMA_NumForeSmoothing = 0 .. _SUMA_NumFinalSmoothing: :ref:`SUMA_NumFinalSmoothing (env)`: Number of smoothing operations to run on final set of mixed colors. This would be the mixed foreground and background colors default value: SUMA_NumFinalSmoothing = 0 .. _SUMA_ColorMixingMode: :ref:`SUMA_ColorMixingMode (env)`: Setup the color mixing mode (ORIG, MOD1) default value: SUMA_ColorMixingMode = ORIG .. _SUMA_AFNI_TCP_PORT: :ref:`SUMA_AFNI_TCP_PORT (env)`: ** OBSOLETE: Port for communicating with AFNI Listening ports are derived from SUMA_AFNI_TCP_PORT Listening port i SUMA_AFNI_TCP_PORT + i (i > 0) default value: SUMA_AFNI_TCP_PORT = 0 .. _SUMA_WarnBeforeClose: :ref:`SUMA_WarnBeforeClose (env)`: Warn before closing with the Escape key (YES/NO) default value: SUMA_WarnBeforeClose = YES .. _SUMA_MaskZero: :ref:`SUMA_MaskZero (env)`: Mask node values 0 ? YES/NO default value: SUMA_MaskZero = YES .. _SUMA_AbsThreshold: :ref:`SUMA_AbsThreshold (env)`: Threshold if Val < thr (NO) or | Val | < | Thr | (YES) default value: SUMA_AbsThreshold = YES .. _SUMA_ThresholdScalePower: :ref:`SUMA_ThresholdScalePower (env)`: Threshold scale precision. 2 is the minimum allowed. This value might be overriden in SUMA. default value: SUMA_ThresholdScalePower = 2 .. _SUMA_CenterOnPatch: :ref:`SUMA_CenterOnPatch (env)`: Center of Rotation is based on nodes used in the mesh and not on all the nodes in NodeList default value: SUMA_CenterOnPatch = NO .. _SUMA_UseCrossTicks: :ref:`SUMA_UseCrossTicks (env)`: Use cross ticks on axis ? default value: SUMA_UseCrossTicks = NO .. _SUMA_1D_Transpose_Warn: :ref:`SUMA_1D_Transpose_Warn (env)`: Warn if 1D file looks like it needs a transpose default value: SUMA_1D_Transpose_Warn = YES .. _SUMA_AdjustMouseMotionWithZoom: :ref:`SUMA_AdjustMouseMotionWithZoom (env)`: Adjust roation and translation factor of mouse with changes in zoom levels default value: SUMA_AdjustMouseMotionWithZoom = YES .. _SUMA_ViewOrthographicProjection: :ref:`SUMA_ViewOrthographicProjection (env)`: Use orthographic projection default value: SUMA_ViewOrthographicProjection = NO .. _SUMA_KeyZoomGain: :ref:`SUMA_KeyZoomGain (env)`: Percent gain for zooming in and out with the 'z' and 'Z' keys. Typical range from 0 to 50 default value: SUMA_KeyZoomGain = 5 .. _SUMA_FOV_Original: :ref:`SUMA_FOV_Original (env)`: Original FOV. Set between 1.0 and 100.0 Default is 30.0, -1 == auto default value: SUMA_FOV_Original = -1 .. _SUMA_Position_Original: :ref:`SUMA_Position_Original (env)`: Original windows size and width in pixels Allowed values are: 'TopLeft' 'RightOffset' 'X Y' Sets only the position to top left corner 'X Y Xwidth Ywidth' Set also width of window default value: SUMA_Position_Original = TopLeft .. _SUMA_Light0Color: :ref:`SUMA_Light0Color (env)`: light0 color default value: SUMA_Light0Color = 1.0,1.0,1.0 .. _SUMA_AmbientLight: :ref:`SUMA_AmbientLight (env)`: Ambient light default value: SUMA_AmbientLight = 1.0,1.0,1.0 .. _SUMA_AllowDsetReplacement: :ref:`SUMA_AllowDsetReplacement (env)`: Allow for replacement of pre-loaded dsets default value: SUMA_AllowDsetReplacement = YES .. _SUMA_AlwaysAssignSurface: :ref:`SUMA_AlwaysAssignSurface (env)`: Allow a dataset to be assigned to a surface, even if domain of dset is specified and different for the surface. default value: SUMA_AlwaysAssignSurface = YES .. _SUMA_ShareGrandChildrenOverlays: :ref:`SUMA_ShareGrandChildrenOverlays (env)`: Allow for surfaces with same DomainGrandParentID to share overlays default value: SUMA_ShareGrandChildrenOverlays = NO .. _SUMA_SnapshotOverSampling: :ref:`SUMA_SnapshotOverSampling (env)`: Increase the resolution of images recorded with 'r' button. Increase is done by taking multiple shots that once stitched together form a high-resolution image. The maximum resolution is set by the GL_MAX_VIEWPORT_DIMS of your graphics card. I have 4096 pixels. If you exceed this number, SUMA will make adjustments automatically. Assemble images with program imcat. default value: SUMA_SnapshotOverSampling = 1 .. _SUMA_NoDuplicatesInRecorder: :ref:`SUMA_NoDuplicatesInRecorder (env)`: Ignore consecutive duplicate images in recorder default value: SUMA_NoDuplicatesInRecorder = YES .. _SUMA_START_NIML: :ref:`SUMA_START_NIML (env)`: start NIML (can't do this for more than one suma at a time!) default value: SUMA_START_NIML = YES .. _SUMA_AllowFilenameDsetMatch: :ref:`SUMA_AllowFilenameDsetMatch (env)`: Allow (YES) datasets with the same filename but differing ID to be considered the same. This is only useful with SUMA_AllowDsetReplacement default value: SUMA_AllowFilenameDsetMatch = YES .. _SUMA_FreezeFOVAcrossStates: :ref:`SUMA_FreezeFOVAcrossStates (env)`: Freeze zoom across states default value: SUMA_FreezeFOVAcrossStates = NO .. _SUMA_DsetColorMap: :ref:`SUMA_DsetColorMap (env)`: Dset color map default value: SUMA_DsetColorMap = Spectrum:red_to_blue .. _SUMA_ShowOneOnly: :ref:`SUMA_ShowOneOnly (env)`: Show only selected dset in suma's surface controller. default value: SUMA_ShowOneOnly = YES .. _SUMA_GraphHidden: :ref:`SUMA_GraphHidden (env)`: Update graphs, even SUMA_ShowOneOnly (or suma's '1 Only') is turned on. default value: SUMA_GraphHidden = YES .. _SUMA_ColorMapRotationFraction: :ref:`SUMA_ColorMapRotationFraction (env)`: Fraction of colormap to rotate with up/down arrow keys. default value: SUMA_ColorMapRotationFraction = 0.05 .. _SUMA_SurfContFontSize: :ref:`SUMA_SurfContFontSize (env)`: Size of surface controller font. Values are SMALL, BIG (old style). default value: SUMA_SurfContFontSize = SMALL .. _SUMA_StartUpLocation: :ref:`SUMA_StartUpLocation (env)`: Where to position SUMA window when first opened. Values are POINTER (at the mouse pointer's location) DEFAULT (let the window manager decide) default value: SUMA_StartUpLocation = DEFAULT .. _SUMA_KeyNodeJump: :ref:`SUMA_KeyNodeJump (env)`: Numer of nodes to jump with the 'alt+arrow' keys. Valid range from 1 to 10 default value: SUMA_KeyNodeJump = 1 .. _SUMA_DriveSumaMaxWait: :ref:`SUMA_DriveSumaMaxWait (env)`: Numer of seconds to wait for SUMA to respond to DriveSuma. Valid range from 0 to 60000, see also env SUMA_DriveSumaMaxCloseWait default value: SUMA_DriveSumaMaxWait = 300.0 .. _SUMA_LEFT_FILE_DSET_IDENTIFIER: :ref:`SUMA_LEFT_FILE_DSET_IDENTIFIER (env)`: String to use in creating left hemisphere dataset wildcards. default value: SUMA_LEFT_FILE_DSET_IDENTIFIER = *lh*.dset .. _SUMA_RIGHT_FILE_DSET_IDENTIFIER: :ref:`SUMA_RIGHT_FILE_DSET_IDENTIFIER (env)`: String to use in creating left hemisphere dataset wildcards. default value: SUMA_RIGHT_FILE_DSET_IDENTIFIER = *rh*.dset .. _SUMA_LEFT_FILE_ROI_IDENTIFIER: :ref:`SUMA_LEFT_FILE_ROI_IDENTIFIER (env)`: String to use in creating left hemisphere roi wildcards. default value: SUMA_LEFT_FILE_ROI_IDENTIFIER = *lh*.roi .. _SUMA_RIGHT_FILE_ROI_IDENTIFIER: :ref:`SUMA_RIGHT_FILE_ROI_IDENTIFIER (env)`: String to use in creating right hemisphere roi wildcards. default value: SUMA_RIGHT_FILE_ROI_IDENTIFIER = *rh*.roi .. _SUMA_LEFT_FILE_OTHER_IDENTIFIER: :ref:`SUMA_LEFT_FILE_OTHER_IDENTIFIER (env)`: String to use in creating left hemisphere roi wildcards. default value: SUMA_LEFT_FILE_OTHER_IDENTIFIER = *lh* .. _SUMA_RIGHT_FILE_OTHER_IDENTIFIER: :ref:`SUMA_RIGHT_FILE_OTHER_IDENTIFIER (env)`: String to use in creating right hemisphere roi wildcards. default value: SUMA_RIGHT_FILE_OTHER_IDENTIFIER = *rh* .. _SUMA_ConvexityDsetOpacity: :ref:`SUMA_ConvexityDsetOpacity (env)`: Initial Convexity Datasest opacity. default value: SUMA_ConvexityDsetOpacity = 0.85 .. _SUMA_ShowLabelDsetAtStartup: :ref:`SUMA_ShowLabelDsetAtStartup (env)`: Display mode of Label Datasest specified in spec file at startup. 'YES' or 'Col': Shows it in color 'Con': Shows only contours (see also env SUMA_ContourThickness). 'C&C': Shows both colors and contours 'XXX'or 'No': Does not show it. default value: SUMA_ShowLabelDsetAtStartup = XXX .. _SUMA_ShowLabelsAtCrossHair: :ref:`SUMA_ShowLabelsAtCrossHair (env)`: Show label at cross hair in viewer You can toggle the display at such labels with F9 default value: SUMA_ShowLabelsAtCrossHair = YES .. _SUMA_LabelDsetOpacity: :ref:`SUMA_LabelDsetOpacity (env)`: Initial Label Datasest opacity. default value: SUMA_LabelDsetOpacity = 0.2 .. _SUMA_AttemptTalkRecover: :ref:`SUMA_AttemptTalkRecover (env)`: Attempt to recover from AFNI <--> SUMA disconnection bug. default value: SUMA_AttemptTalkRecover = Yes .. _SUMA_CmapsDir: :ref:`SUMA_CmapsDir (env)`: Name of directory containing user's own SUMA color maps (`*`.cmap) default value: SUMA_CmapsDir = None .. _SUMA_RetinoAngle_DsetColorMap: :ref:`SUMA_RetinoAngle_DsetColorMap (env)`: Name of color map for datasets of retinotopy angles. These would be produced by 3dRetinoPhase default value: SUMA_RetinoAngle_DsetColorMap = rgybr20 .. _SUMA_VFR_DsetColorMap: :ref:`SUMA_VFR_DsetColorMap (env)`: Name of color map for VFR datasets produced by SurfRetinoMap default value: SUMA_VFR_DsetColorMap = afni_n2 .. _SUMA_NodeCoordsUnits: :ref:`SUMA_NodeCoordsUnits (env)`: Coordinate units of surface nodes. Choose from 'mm' or 'cm' A bad choice can make the surfaces render with many artifacts. default value: SUMA_NodeCoordsUnits = mm .. _SUMA_DoNotSendStates: :ref:`SUMA_DoNotSendStates (env)`: Which anatomically correct surf. states should not NOT be sent to AFNI? This is mostly for deciding whether one of 'white' or 'smoothwm' FreeSurfer states should not be sent to AFNI. The default is to let them all go. You can specify multiple states with a , delimited list (no spaces!). By default nothing is excluded. default value: SUMA_DoNotSendStates = N/A .. _SUMA_AutoRecordPrefix: :ref:`SUMA_AutoRecordPrefix (env)`: Prefix for autorecord (suma's Ctrl+R) files. FreeSurfer states should not be sent to AFNI. Add a path if you want the files to endup in a particular directory. You can also add an extension to prefix to specify the output type. Choose from .jpg, .ppm, or .1D . The fallback type is .jpg default value: SUMA_AutoRecordPrefix = ./SUMA_Recordings/autorecord.jpg .. _SUMA_CrossHairLabelFont: :ref:`SUMA_CrossHairLabelFont (env)`: Font for cross hair label in SUMA viewer Choose one of: f8 f9 tr10 tr24 he10 he12 he18 default value: SUMA_CrossHairLabelFont = f9 .. _SUMA_IxT_LinkMode: :ref:`SUMA_IxT_LinkMode (env)`: Linking mode of I and T sub-brick selectors Choose one of: None, Same, Stat default value: SUMA_IxT_LinkMode = Stat .. _SUMA_ArrowFieldSelectorTrigger: :ref:`SUMA_ArrowFieldSelectorTrigger (env)`: Minimum Number of sub-bricks to trigger use of arrow field for sub-brick selectors. default value: SUMA_ArrowFieldSelectorTrigger = 200 .. _SUMA_Sym_I_Range: :ref:`SUMA_Sym_I_Range (env)`: Use symmetric Intensity range at startup? Valid options are: YES or NO: For your preference if no decision is made by the software FYES or FNO: To force your preference and keep software from deciding default value: SUMA_Sym_I_Range = YES .. _SUMA_Auto_I_Range: :ref:`SUMA_Auto_I_Range (env)`: Set auto Intensity range by default (YES or NO) default value: SUMA_Auto_I_Range = NO .. _SUMA_Auto_B_Range: :ref:`SUMA_Auto_B_Range (env)`: Set auto Brightness range by default (YES or NO) default value: SUMA_Auto_B_Range = NO .. _SUMA_ContourThickness: :ref:`SUMA_ContourThickness (env)`: Set thickness of dataset contours default value: SUMA_ContourThickness = 1.0 .. _SUMA_LHunify: :ref:`SUMA_LHunify (env)`: Merge separated left/right states for inflated/spherical/etc. surfaces Choose from YES or NO default value: SUMA_LHunify = YES .. _SUMA_SameSurfCont: :ref:`SUMA_SameSurfCont (env)`: Put surface controllers in same window Choose from YES or NO default value: SUMA_SameSurfCont = YES .. _SUMA_WindowOffset: :ref:`SUMA_WindowOffset (env)`: Adjust offset of Surface Viewers as they are first open Choose from AUTO or provide two X Y offsets. default value: SUMA_WindowOffset = Auto .. _SUMA_LockViewers: :ref:`SUMA_LockViewers (env)`: Lock views across viewers Choose from YES or NO. default value: SUMA_LockViewers = YES .. _SUMA_VO_ColorMap: :ref:`SUMA_VO_ColorMap (env)`: Set colormap for volumes, choose any of the standard list default value: SUMA_VO_ColorMap = bw20 .. _SUMA_VO_Reorient: :ref:`SUMA_VO_Reorient (env)`: Force reorienting of read volume. To force reorientation, Choose from RAI, LPI, RAS. etc... Use NO to avoid reorientation. This env. is for debugging purposes. default value: SUMA_VO_Reorient = NO .. _SUMA_DriveSumaMaxCloseWait: :ref:`SUMA_DriveSumaMaxCloseWait (env)`: Set maximum waiting time for proper detection of closed stream This is to avoid DriveSuma's: Failed to detect closed stream ... complaint which results in a forced stream closing. Time unit is in seconds. See also env SUMA_DriveSumaMaxWait default value: SUMA_DriveSumaMaxCloseWait = 5 .. _SUMA_ObjectDisplayOrder: :ref:`SUMA_ObjectDisplayOrder (env)`: Set order in which object types are rendered. This order will affect the resultant image in the few instances where alpha transparency is used. The order can be specified for only three types of objects for now: graphs, surfaces, and volumes. If you want to render graphs first, followed by volumes then surfaces then set SUMA_ObjectDisplayOrder to something like: 'graph,vol,surf'. Do not include spaces between the type names. default value: SUMA_ObjectDisplayOrder = vol,surf,graph .. _SUMA_Dset_Font: :ref:`SUMA_Dset_Font (env)`: Font for datasets in SUMA viewer Choose one of: f8 f9 tr10 tr24 he10 he12 he18 default value: SUMA_Dset_Font = f9 .. _SUMA_Dset_NodeConnections: :ref:`SUMA_Dset_NodeConnections (env)`: Method for representing connections to a certain node in a graph dataset. Choose one of: Edge, Color, Radius, C&R, XXX default value: SUMA_Dset_NodeConnections = Edge .. _SUMA_VO_InitSlices: :ref:`SUMA_VO_InitSlices (env)`: Set which slices should be shown when a volume is first loaded. You can set parameters for each of the Ax, Sa, and Co planes, and the volume rendering. Each plane gets its own string formatted as such: PL:SL:MON:INC where: PL is the plane (Ax, Co, Sa, or Vr) SL is the slice number, you can also set the number as a fraction of the number of slices in the volume. MON is the number of montage slices INC is the increment between montage slices. You can use fractions for this parameter also. If you want to set parameters for a certain plane, but do not want to see it, prepend the plane name with 'h' (for hide) as in 'hAx' Note that for Vr, there are no SL, MON, and INC qualifiers Also, SUMA will force the display of at least one plane because otherwise you have no way of opening a volume controller Example: 'Ax:0.5:3:10,Co:123:2:50,Vr' default value: SUMA_VO_InitSlices = Ax:0.5,Sa:0.5:2:0.5,hCo:0.5 .. _SUMA_VrSelectable: :ref:`SUMA_VrSelectable (env)`: Allow selection of voxels on 3D rendering. Choose one of: YES or NO default value: SUMA_VrSelectable = YES .. _SUMA_HomeAfterPrying: :ref:`SUMA_HomeAfterPrying (env)`: Perform 'Home' call in SUMA after each prying. If YES, objects are repositioned to stay in the middle of the viewer as you pry the surfaces apart. This behavior is desired in general, unless you don't like the initial positioning in the first place. Choose from YES or NO default value: SUMA_HomeAfterPrying = YES .. _SUMA_SUMA_TESSCON_AutoScale: :ref:`SUMA_SUMA_TESSCON_AutoScale (env)`: Assume surface in TESSCON units if range is extreme If YES, surfaces with a big difference between max and min dims are scaled by 319.7. Don't set this env to YES unless this jibber jabber means. Choose from YES or NO default value: SUMA_SUMA_TESSCON_AutoScale = NO .. _SUMA_CountProcs_Verb: :ref:`SUMA_CountProcs_Verb (env)`: Turn on verbose mode for function count_procs() that checks for recursive calls to a program. Do not keep this env set to YES unless you are debugging. default value: SUMA_CountProcs_Verb = NO .. _SUMA_Transparency_Step: :ref:`SUMA_Transparency_Step (env)`: Number of transparency levels to jump with each 'o' key press Choose one of 1, 2, 4, or 8 default value: SUMA_Transparency_Step = 4 .. _SUMA_AutoLoad_Matching_Dset: :ref:`SUMA_AutoLoad_Matching_Dset (env)`: If YES, then automatically load datasets with names matching those the surface just read. For example, if you load a surface named PATH/TOY.gii, for instance, and there exists a file called PATH/TOY.niml.dset then that file is automatically loaded onto surface TOY.gii. This would work for all surface types (e.g. TOY.ply) and dataset types (e.g. TOY.1D.dset) Choose from YES or NO default value: SUMA_AutoLoad_Matching_Dset = YES .. _SUMA_Classic_Label_Colors: :ref:`SUMA_Classic_Label_Colors (env)`: Colorize labeled datasets without attempting to make colors match what would be displayed in AFNI (YES or NO). Set to YES to match old style colorization preceding the addition of this variable default value: SUMA_Classic_Label_Colors = NO .. _SUMA_Range_Multiplier: :ref:`SUMA_Range_Multiplier (env)`: Multiplier for range of thresholding scale. default value: SUMA_Range_Multiplier = 1.0 .. _SUMA_pval_at_switch: :ref:`SUMA_pval_at_switch (env)`: Default p value to adopt when switching to a new sub-brick. Negative values mean leave the threshold alone when switching. default value: SUMA_pval_at_switch = -1.0 .. _SUMA_DriveSumaQuiet: :ref:`SUMA_DriveSumaQuiet (env)`: If YES, then reduce messages to only errors while driving suma Choose from YES or NO default value: SUMA_DriveSumaQuiet = NO .. _SUMA_SHOWPOPUPS: :ref:`SUMA_SHOWPOPUPS (env)`: If YES, then show popup message windows in suma Choose from YES or NO default value: SUMA_SHOWPOPUPS = NO Current Version Info: Compile Date: Dec 19 2018