5.1.3. AFNI GUI: Image window

AFNI GUI: Image Window
Load a dataset and open an image viewer.

Image Window

Basics

Click and release mouse button 1 (left button) to move the crosshairs to the location of the cursor. Click down Button 1 (left button) in the image window and hold it down, then drag around while holding. This changes contrast and brightness. You must move cursor a small distance while doing click-and-hold before the contrast/brightness change starts. Scroll-wheel in the image window moves through slices. Keyboard ALT (⌘ on macOS) while using the scroll-wheel in the image window will change the functional overlay threshold slider in the main AFNI GUI window. This action affects all image viewers in the current AFNI controller. Shift+button 2 will allow you to drag crop a region. (The middle button on a 3 button mouse, or click down on the scroll-wheel, or shift+option on macOS.) Keyboard shortcuts are listed here. Clusterize shortcuts (these have a cool animation effect): j = Jump to the nearest cluster’s peak (or center of mass) f = Flash current cluster if the crosshairs are inside one. n or N = Jump to the next or previous cluster’s peak or center of mass.

Crosshairs
Crosshairs in image window show current focus location (xyz in AFNI controller) Also show the cut planes for the other image viewers (in this case the sagittal and coronal viewers) Can control crosshair color and gap size from main AFNI controller. (see here). When using image montage, other viewers show multiple crosshairs. (see here).

Hidden Image Popup Menu

Hidden image popup menu using Button 3 or right-click over the actual image. May need its own page to show some examples. InstaCorr Set InstaCorr SeedJump Jumpback lets you jump the focus position back to its last place. Useful for when you click in the wrong place and get lost. Jump to (xyz) lets you enter xyz-coordinates (in mm), and then the focus position will jump there. (3 numbers , or space separated) External programs 3dclust and others can generate xyz coordinates of interest. Once you have +tlrc dataset, can jump to regions from Talairach atlas. Jump to (ijk UL) lets you jump to a particular voxel index location in the underlay coordinate system. (Dialog box is similar to Jump to (xyz)) Jump to (ijk OL) lets you jump to a particular voxel index location in the overlay coordinate system. (Dialog box is similar to Jump to (xyz)) Jump to (Cluster) -Go to atlas location -Where Am I? -Atlas Colors Image display lets you turn control widgets on and off to unclutter screen a little; useful if you want to make a screenshot. But use the Sav1 button instead of a screenshot. (see here) Edit Environment Draw ROI plugin bg =x (x is some number)

Slider

The slider below image lets you move between slices. The number above the slider indicates the current displayed slice. (in this case 144) Leftclick and drag to move past many slices. Leftclick ahead or behind to move 1 image at a time. Hold button click down to scroll continuously through slices. Middle click (option+left click on macOS if you set it up in XQuartz) in ‘trough’ to jump quickly to a given location. Mouse scroll-wheel action when cursor is over image also changes slices. ctrl+click will jump to the start of end of the slices, depending on which side of slider you click.

Vertical Intensity Bar

Vertical intensity bar to right of image shows mapping from numbers stored in image to colors shown on screen. Bottom of intensity bar corresponds to smallest numbers displayed. Top corresponds to largest numbers displayed (popup hint shows numerical range) Smallest-to-largest display range is selected from the Disp control panel. (see here), or from the right click hidden popup menu (see here). Scroll-wheel in the intensity bar changes contrast. ALT (⌘ on macOS) plus scroll-wheel in intensity bar changes brightness. All image viewers from all AFNI controllers use the same intensity bar. When you change intensity scale in one viewer, all others viewers change. Unless AFNI is started with the -uniq command line option, in which case each AFNI controller’s viewers have independent intensity bars. But all image viewers from same controller always share same intensity bar.

Colr, Swap, Norm, .etc

Colr changes grayscale to color spectrum, and back (fun & useless). Swap swaps top of intensity bar with bottom. Norm returns the intensity bar to normal (after you mess it up). c controls contrast. b controls brightness. Useful combination c ↑ 2-3 times, b ↓ 2-3 times. r rotates the intensity bar (also fun & useless). g changes the gamma factor (nonlinearity) for the intensity bar. i changes the size of the image in the window. 9 changes the opacity of the color overlay. (This control only present for X11 TrueColor displays does this matter anymore?) z zooms out and in. pan lets you pan around when zoomed in. (greyed out if not zoomed) crop lets you crop the image viewing area. Card or Obliq (not a button) tells you if the dataset axes are parallel to LR-AP-IS or not parallel. At bottom right, the arrowpad controls the crosshairs. Arrows move 1 pixel in that direction for the current window. Central button closes and opens crosshair gap (for fine control of the crosshairs location) For more crosshairs controls see here.

Disp

Disp controls the way images are displayed and saved. This may need to go on its own page! It pops up its own control window and most controls change image immediately. Orientation controls at top allow you to flip image around. + LR Mirror flips the image left to right. For example, if the image was displayed left=Left it will flip to left=Right No Overlay lets you turn color overlays off (crosshairs; function) Min-to-Max Intensity bar is data min-to-max. 2%-to-98% Intensity bar is smallest 2% of data to largest 98%. This avoids having a few very bright voxels dominate intensity scaling. Free Aspect lets you distort image shape freely. Otherwise, AFNI tries to keep image shape true as you stretch/shrink window. The save panel controls how images are saved to disk. For more details, (see below) All buttons off: saved image file contains slice raw data. (not what you want) Nsize Save: same, but images are 2N in size. PNM Save: images are saved in PPM/PGM format (color/gray). Save to .xxx(s): saves image(s) to specified format. Save One: for saving montage. Save Anim GIF will save an animated .gif file scrolling through the slices of the image. Project applies a projection function to plus-or-minus ‘Slab’ images from each pixel. Slab +- selects the number of slices around the current view to use for the projection. Useful for looking at blood vessels and other different images. Tran 0D lets you transform voxel values before display. Log10 and SSqrt are useful for images with extreme values. Tran 2D provides some 2D image filters for the underlay only. Median 9 smoothing can be useful for printing images. RowGraphs are plots of the underlay (grayscale) image intensity as x vs. y graphs. Each graph is from one displayed horizontal row of the image. The bottom rowgraph is from the image row under the crosshairs. Upper rowgraphs are from higher image rows. Image transformation functions and image rotation/flips will affect the rowgraphs as well as the image display. The color marker indicates the crosshair focus point and can be hidden with the No Overlay button. If you want columns, flip the image with CCW 90. Surfgraph lets you graph the voxel values in a surface graph. Extra imaging processing filters are provided at the bottom. Sharpen is sometimes useful for deblurring images. Edge Detect is useful as the underlay for checking alignment.

Sav1.jpg

Sav1.jpg lets you save images from viewer to disk files. Image files are saved in your current working directory. The saved image is on the matrix of the dataset. It is NOT a screen capture; that is, the image saved will not depend on the size of the image viewer window or the resolution of the screen. The crosshairs will be captured with the image unless you turn it off. (see here on how to do that) The Prefix is the name of the image file you want to save without the extension. afni will append the extension of your chosen format. If you use the same prefix more than once, afni will overwrite the image saved to disk without warning. Blowup causes an explosion in your computer, destroying all work! just checking to see if anyone reads this… Actually Blowup artificially increases the size/resolution of the output image by a factor of your choosing from 1 to 8. This is useful for outputting pretty images for all of the papers you are going to publish (while also citing AFNI) See here on how to cite AFNI. The .jpg will change with your choice of output format. (for example it might be Sav1.bmp for a bitmap image) To change the format, right click the Sav1.jpg button to get this popup: Selecting Sav:aGif will save an animated .gif file scrolling through the slices of the image. Selecting this will change the saveing dialog box adding a From: and To: indicating the slices that you want. Warning: Images are saved as sent to the viewer, not as displayed. Means that aspect ratio of saved image may be wrong. (non-square pixels) This can be fixed with Define Datamode ⇒ Warp Anat on Demand (see here). Or by setting AFNI_IMAGE_SAVESQUARE to YES (see here).

Montage

Mont lets you display a rectangular layout of images (i.e., montage). Across and Down determine number of sub-images shown. Spacing determines how far apart the selected slices are Every nth slice, for n = 1, 2, … Multiple crosshairs in other image viewers will show montage slices. Border lets you put some blank pixels between sub-images. Color lets you choose the color of the border pixels. At bottom row, the action buttons cause something to happen: Quit closes the Montage control window. 1x1 changes Across and Down back to 1. Draw actually causes the montage to be drawn. Set ⇔ Draw then Quit In this example, we have selected a 2 by 2 montage showing every other slice with a 1 pixel yellow border.

Rec

Rec lets you record images for later saving. So you can build a sequence of images using any set of AFNI controls. You can change color maps, functional thresholds, datasets, … then save them to disk for animation, etc. The Rec button button pops down a menu that sets the record mode. The top section controls WHEN images will be recorded into the sequence. Off ⇒ recording is off… Next One ⇒ the next image displayed is recorded, then back to Off. Stay On ⇒ record each image when displayed. The bottom options control WHERE new images are to be stored into the sequence. After End = at the tail of the sequence. Before Start = at head of sequence. Insert -- = insert before current sequence position. Insert ++ = insert after current sequence position. OverWrite = replace current sequence position. -- OverWrite = replace image before current position. ++ OverWrite = replace image after current position. Recorded images go into a special new image viewer. The slider moves between recorded images. Kill deletes 1 image from recorded sequence. Save will save record images. (files with the same prefix will be overwritten without warning. Right click on Save to change the output image format. Your choice of formats is not saved after you close this special viewer. So remember to change this each time you start. aGif is a good choice. If you leave it on .jpg you will get a single jpeg file for each item in the sequence. You may want to set Xhairs to Off on the AFNI control panel before recording images. Done closes the recorded image viewer. Remember to click Done before you start doing anything else as this will keep recording forever! Here is a simple example output: If Unix programs whirlgif and/or gifsicle are installed on your system, AFNI can write GIF animations directly (e.g., for fun Web pages). If program mpeg_encode is installed, AFNI can write MPEG-1 animations. Source code for these free programs is included with AFNI source code.

Jump within GUI Guide

Starting	Main controller	Image window	Graph window
Overlay panel	Datamode panel	Chooser menu	Maps