5.1.4. AFNI GUI: Graph window

Open Some Graph Windows

Graph buttons for the adjacent views (Axial, Sagittal, Coronal) Normal: button opens a viewing window Inverted: button raises opened window Right-click on an inverted button ‘fetches’ the graph window Graph buttons are usually only meaningfull if the selected underlay dataset has a time index (usually some functional image) Graph buttons are only enabled for datasets that are viewing their data files directly Not warping on demand – see the top of the Define Datamode control panel (see here)

Graph Window

Graph viewer takes voxel values from same dataset as image viewer If dataset has only 1 sub-brick, graph viewer only shows numbers (Not very useful unless you are an MRI physics type, perhaps) To look at images from one dataset locked to graphs from another dataset, must use 2 AFNI controllers and Define Datamode ⇒ Lock on AFNI control panel Keystrokes in graphs that have no menu items are: < or , or left-arrow keys move the time index down by one. > or . or right-arrow keys move the time index up by one. L turns off/on the AFNI logo in the lower left corner. The following are video mode operations moving the cursor through the time index. An easy way to animate an EPI time series, to look for subject motion. v moves through the data forwards and jumps back to the start of the graphs when it gets to the last time index. V is the same only it moves the cursor backwards. r moves forwards but bounces back from the last time index. R moves backwards and bounces back from the first time index. Link to all graph window keyboard shortcuts

If graph and image viewer in same slice orientation are both open, crosshairs in image window change to show a box containing dataset voxels being graphed

Central sub-graph (current focus location) is outlined in yellow Current time index is marked with small red diamond on data graph Left-clicking in a non-central sub-graph moves that location to focus. Making it the yellow center sub-graph and moving the crosshairs on the image window to match the new location. Left-clicking in central sub-graph moves time index to nearest point Can also use Index control in AFNI controller to change time Right-clicking in any sub-graph pops up some statistics of its data

Left-clicking the icon in the lower left corner causes icon and menu buttons to disappear. Useful if you want to do a screenshot to save AFNI window(s) Left-clicking in same place will bring icon and buttons back

Opt Menu

Opt menu buttons let you control how graphs appear Many items have keyboard shortcuts Make sure you are typing into the correct window! (XQuartz on macOS makes the button difficult to read…)

Index Pin/Stride

Index Pin/Stride changes which data points are displayed in the graph. Useful when switching between datasets of different lengths. (note to staff: this is not in the gui button help) The defaults (0, 0, 1) show all data points in the dataset. Bot... sets which data point is the first (on the left) Top... sets which data point is the last (on the right) The number displayed will be your choosen number - 1 Stride sets the interval of data points displayed. This number will auto correct to fit your other choices. For example, if the data has 151 time points, setting Bot... = 10, Top... = 100, Stride = 9 will get you a graph that shows every 9th data point from the 10th to the 99th.

Scale

Scale changes scale of graphs. Mapping from voxel values to screen pixels. Down [-] and Up [+] shrinks or expands the graphs vertically. Choose lets you pick exact scale factor. Positive (pix/datum) = number of y screen pixels for each change of 1 in data. Negative (datum/pix) = size of change in data to get 1 y screen pixel. Auto [a] makes AFNI pick a nice scale factor (this one time) AUTO [A] autoscale the graphs (every time they are redrawn) Scale factor does not change when you resize graph,change matrix, etc. You usually have to auto-scale [a] or [A] afterwards. Current scale factor is shown below graphs:

Matrix
Matrix changes number of sub-graphs across each row and column. Down [m] and Up [M] decrease and increase number. # lets you pick number exactly with allowable matrix sizes between 1 and 21

Grid

Grid lets you change spacing of vertical grid lines (yellow in color by default). Useful for showing regular timing interval (e.g., block timings) Down [g] and Up [G] decrease and increase the spacing. AutoGrid lets AFNI choose something reasonable (default) Choose lets you pick the number exactly. HorZ [h] will put in a dashed line at the y = 0 level in sub-graphs. Only useful if data range spans negative and positive values! Current grid spacing is shown below graphs.

Slice
Slice lets you change slices Down[z] and Up[Z] move one slice Can also choose slice directly from menu Current voxel indexes are shown below graphs: Corresponds to [Voxel Coords?] display in AFNI controller (from Define Datamode ⇒ Misc menu see here)

Colors, Etc.

Colors, Etc. lets you alter the colors/lines used for drawing. Lines used for sub-graph frame boxes, grid lines, data graphs, FIM orts/ideals, and double plots can have color changes and be made thicker. Grid color is also used to highlight central sub-graph. Can choose to graph curves as lines, points, or both together Can change color of background and text Can change gap between sub-graph boxes Play with it and see what you can make!

Baseline

Baseline [b] changes how the sub-graphs are plotted. All sub-graphs have same scale factor, to convert values into vertical pixels. Baseline is value that gets plotted to bottom of sub-graph. Individual: all sub-graphs have different baselines Baseline = smallest value in each displayed time series This can be confusing; same vertical location doesn’t mean same value Shown below graphs as Base: separate Common: all sub-graphs shown at any one time get same baseline Baseline = smallest value in all displayed time series Shown below graphs as Base: common May need to rescale [a] after changing baseline Global: all sub-graphs get same baseline even when spatial position changes Default global level is smallest value in entire dataset Set from [Baseline] ⇒ [Set Global] menu item Range of central sub-graph is shown to left of graph region Central sub-graph bottom (baseline) value is shown at lower left Upper left shows value at top of central sub-graph box Number in [brackets] shows data range of one sub-graph box’s height If baselines are separate, bot/top values only apply to central sub-graph. Baseline mode is displayed at the bottom of the graph window.

Show Text?

Show Text? [t] allows you to see text display of values instead of graphs. The number shown will be the numerical value at that voxel for the current time index. The display at the bottom of the graph will show info for the central sub-graph. In the below example, the values are: indx=13 [#14] is the current time index (and sub-brik). val=261 is the numerical value of the voxel at the central sub-graph. @t=29.15151 is the time value calculated from the TR of the dataset. (provided there is a TR in the dataset header information).

Thresh Fade?

Thresh Fade? [F] marks sub-graphs of those voxels that are below threshold. (note to staff: this is not in the gui button help) Those sub-graphs for voxels that are un-colored when See Overlay is turned on will be greyed out. Fading is only on when See Overlay is on and with Clusterize and InstaCorr. If Fading is on, there is an indicator at the bottom of the graph window. The sub-plots are data from the underlay with fading from the thresholded overlay. The red and blue text in the sub-graphs in the below example are just for emphasis…

Save Image
Save Image [S] lets you save a snapshot of the graph window to an image file. The image will be saved into your current directory. (where you started afni) If you don’t provide an extension (.jpg or .png), the image will be saved as a .ppm file (Portable Pixmap Format). If you use .jpeg as the extension, you will still get .ppm

Write Center

Write Center [w] lets you write data from central sub-graph to a file. The file is in ASCII format that can be imported into other programs The filename is of the form xxx_yyy_zzz.suffix.1D (using voxel indexes) The Set 'w' Suffix dialog lets you add text after the xxx_yyy_zzz and before the .1D file extension separated by .. For example if you set your suffix as my_data, and the central sub-graph is at the voxel coordinates x=50, y=100, z=150, the file name will be 050_100_150.my_data.1D Write Center will overwrite a file with the same name if it exists in the same directory. So use the set suffix to make sure you don’t lose any data. Once you choose your suffix you will not be able to remove the suffix, only change it to something else (note to staff: may need to fix this)

Tran 0D
Tran 0D lets you transform the data before it is graphed. The chosen function is applied to each point in the time series. Log10 and SSqrt useful for images with extreme values. The below images are before and after a Log10 transformation.

Tran 1D

Tran 1D lets you transform the data before it is graphed. The chosen function is applied to the time series as a whole. You can combine the 0D and 1D transformations if you want to get fancy. Below is the raw data as above with the AdptMean19 transformation. (XQuartz on macOS obscures the text a bit in the lower right corner) Note to staff: Lots of stuff here. How much detail do we want? Is there a good place with documentation? Should we break this section out?

Double Plot
Double Plot lets you plot output of Tran 1D and original data together. Tran 1D must be active to see the transformed data along with the original time series data. Below is the data with Tran 0D set to Log10 and Tran 1D set to AdptMean19 and DPlot On. You can always change the colors with the Colors, Etc. option above. (see here)

Detrend
Detrend changes the order of the time series L1 detrending / baseline removal. -1 is for NO detrending (default).

X-axis
X-axis lets you choose how graph x-axis is chosen The default is linear time. Useful only in very limited circumstances! Below is the same data with X-axis=center (not really sure that is useful with this data…)

Jump within GUI Guide

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