ynicDV3D HELP
Click in the main window to start.
( press 'z' to launch help)
Quick links:

- Using the main window
- Using the side menu
- Loading Data

- fMRI
- MEG (beamforming)
- MEG (dipoles)

- Other data types

- Cortex (brain surface)

- Useful functions

- snapping planes to a selected point
- generating ortho views
- saving out images

- Keyboard shortcut list
- Supported file formats

USING THE MAIN WINDOW: (back to top)
Overview:
The main window will load with 3 planes visible. Co-ordinates of the point you have picked (see LEFT MOUSE BUTTON) are displayed in the bottom left in yellow. If you supplied a transform matrix for this dataset to MNI space on startup the equivalent co-ordinates in the MNI brain are also displayed in red.
Instructions for interacting with the main window:

Key points: Before you start understand this: Mouse clicks can be made inside the edges of the MRI data object or outside. Different mouse buttons do different things, and each mouse button does something different depending on whether you have clicked it inside / outside the edge of the data. Click the mouse button, hold it down and then move the mouse (whilst still holding the button down) to invoke the action. If your mouse's middle button is a wheel, you can (normally) click this is and hold it down like a normal middle mouse button

LEFT MOUSE BUTTON: click, hold down the button and move the mouse

> OUTSIDE the edges of the brain: ROTATE in that direction
> INSIDE the edges of the brain to PICK a co-ordinate of a point on a plane
> Coordinates appear in the bottom left corner of the selected plane

> > ADVANCED: MNI Co-odrinates: when the program starts it asks you to supply (1) a structural volume and (2) optional transformation matrix for this dataset to MNI space. If you supplied an MNI transformation, the equivalent MNI co-ordinates to those you have picked in this dataset are displayed in red

MIDDLE MOUSE BUTTON: click, hold down the button and move the mouse

> OUTSIDE the edges of the brain: MOVE the entire dataset in that direction
> INSIDE the edges of the brain to MOVE THE PLANE backwards or forward: This effectively re-slices the plane to show you a different slice

> > > ADVANCED: RESLICE IN ANY DIRECTION: when you middle click inside the edges of a slice, bounding boxes appear at the edges (the slice edges go green and blue lines appear inside these). Middle clicking in this edge 'box' and moving the mouse rotates the selected slice around its axis. This allows you to reslice in any direction. You can re-centre the slices at any time by pressing 'L' in the main window or selecting the 'RESET' button on the side menu.

RIGHT MOUSE BUTTON: click, hold down the button and move the mouse

> OUTSIDE the edges of the brain: ZOOM IN (top half of window) or ZOOM OUT (bottom half)
> Press r to reset the zoom of the window
> INSIDE the edges of the brain: change the COLOUR LEVEL or WINDOW LEVEL of MRI data

USING THE SIDE MENU (back to top)

Key points: Before you start understand this: The side menu is started when you first left-click in the main window. To use the side menu's functions you must click in the circles / arrows (not the text describing the function). Each function has a description of the keyboard shortcut that can be used after clicking in the main window to do the same thing. This is usually much faster after you become familiar with the program.

The menu has a number of buttons which can be pressed to call the desired functions. You need to click on the actual buttons / arrows (not the text) to call the action.
Each function can also be called by pressing the appropriate keyboard key when the main window has the focus.
Simply click on an object in the Menu Window to call the function.
LOADING DATA ( .. and interacting with it ..) (back to top)
Data files are loaded by calling your system's standard pop-up window file dialog. Simply select the required file and click OK or OPEN when requested.
Data file formats supported at the moment are:

Beamforming results (MEG) | NIFTI compressed (.nii.gz)
fMRI results | NIFTI compressed (.nii.gz)
Structural MRI | NIFTI compressed (.nii.gz)
Dipoles (MEG) | 4D Neuroimaging dipole fit output file (any format)
Fiber data (DTI) | .OUT fiber files (see specification)
Cortical Surface | Binary .OFF files (see specification)

If you have ANALYZE files (.hdr and .img) at the moment you can easily convert them to NIFTI_GZ by running avwchfiletype at the command line ( .. at YNiC ..)

Loading data can take time .. remember that data sets are often big and all the clever things we try to do to display the data also take time. We are always working to make these faster but ( .. in the meantime .. ) please be patient.
Functional data (or those which we typically visualise as 'coloured blobs') can be loaded in 2 different modes, 2D-merged or 3D:

- 2D-merged processing merges the 'blobs' of activation / deactivation into the already loaded structural dataset; absolute thresholds (positive and negative) are set by you when the data is loaded; data needs to be reloaded if thresholds are to be recalculated ...

- 3D processing shows the blobs as 3D surfaces; thresholds are set by you when loading.. in this case the thresholds are not absolute but are as a percentage of the maximum and minimum of your data: e.g. lets say you have a maximum of 20 and a minimum of -10 in your data. You choose to spilt these into 10 'bins' and display the top 5. This will create an isosurface for each of the isocontours at +20, +18, +16, +14 and +12 for your positive values (shades of red-yellow) and -10, -9, -8, -7, and -6 in your negative values (shades of blue). Once the surfaces are genrated they can be cycled on/off so you can see all positive values only, a selection of positive, all negative, a selection of negative or even a selection (e.g. the top 2 of all 5 generated surfaces) of both the top x negative and positive values together ...

LOADING MRI DATA (back to top)
Structural MRIs are loaded at the startup of the program.
fMRI (back to top)
fMRI results are loaded for 2d-merged or 3d visualisation (see Functional data types above)
Press F in the main window or select the LOAD button under FUNCTIONAL DATA on the side menu to load your fMRI result data file
After typing F in the main window or clicking the Load button under FUNCTIONAL DATA on the side menu, you will be prompted to pick:

1. a NIFTI GZ file containing your fMRI results – BROWSE, SELECT A FILE AND CLICK OPEN .. NB: this file should already have been co-registered to the structural data you have loaded at the start of the program. This is usually done by running FSLs FLIRT program. See FSL tutorial.
2. You will now be asked if you want to load the data in 2d-merged or 3d mode (see Functional data types above). Type m if you want 2d-merged mode or 3 if you want 3d mode.
3. If you selected 3d mode:

1. Enter the number of bins you would ike to split your data into (see Functional data types above). The current maximum is 10. CLICK OK
2. Enter the number of these bins you would like to be made visible. CLICK OK .. e.g. if you set 10 before and 3 here, you will see surfaces at 80%, 90% and 100% of the maximum in your data.
3. Give the program a few seconds to draw the surfaces .. this can take up to a minute depending on the number of surfaces you chose to calculate / display
4. The top surface is displayed (or surfaces if there are positive and negative maxima in your dataset). Positive values are displayed inn red-yellow and negative in shades of blue. Since these surface may be small it may be diffucult to see.
5. You can make more surfaces visible by pressing X or clicking the Threshold DOWN button on the side menu .. this effectively lowers your theshold by 10%
6. You can make fewer surfaces visible by pressing Y or clicking the Threshold Up button on the side menu .. this effectively raises your theshold by 10%
7. Press f or click the Cycle 3d button on the side menu to cycle through the following modes:

1. Positive and negative visible (default)
2. Positive only visible
3. Negative only visible
4. Neither visible
5. Back to positive and negative visible ... etc.

8. N.B. whilst cycling through, the threshold may be reset to highest values only, but this can be adjusted as required by pressing X / Y as described above

4. If you selected 2d-merged mode:

1. Prompts will tell you the maxima and minina that have been found in your data files .. if there are no negative values only one pop-up box is used for positive value choices (vica versa)
2. You will be asked to enter the lower boundary (or threshold) of the data to display. Enter the value and click OK. .. e.g. the maximum in your data might be 7.353 but you might only want to threshold the result at all values above 2.3 ( if loading z-stat data for example)
3. The default value in the pop-up box is 'skip'. This allows you to skip the generation of the positive values / negative values ( .. or both! .. ) so that positive or negative results can be viewed independently. Click OK without changing the value if you want to skip.
4. Give the program a few seconds to draw your results .. this can take up to a minute depending on the number of slices in your mri dataset
5. You can toggle between the original structural dataset loaded by pressing M or clicking the Switch 2d button on the side menu

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MEG DATA (back to top)
Loading - Beamforming results (back to top)
Press F in the main window or select the LOAD button under FUNCTIONAL DATA on the side menu to load your beamforming result data file
After typing F in the main window or clicking the Load button under FUNCTIONAL DATA on the side menu, you will be prompted to pick:

1. a NIFTI GZ file containing your beamforming results – BROWSE, SELECT A FILE AND CLICK OPEN .. NB: this file should already have been co-registered to the struturla data you have loaded at the start of the program. This is usually the case for beamforming data - you would only look at the results in subject R1025's directory overlaid on R1025's structural.
2. You will now be asked if you want to load the data in 2d-merged or 3d mode (see Functional data types above). Type m if you want 2d-merged mode or 3 if you want 3d mode.
3. If you selected 3d mode:

1. Enter the number of bins you would ike to split your data into (see Functional data types above). The current maximum is 10. CLICK OK
2. Enter the number of these bins you would like to be made visible. CLICK OK .. e.g. if you set 10 before and 3 here, you will see surfaces at 80%, 90% and 100% of the maximum in your data.
3. Give the program a few seconds to draw the surfaces .. this can take up to a minute depending on the number of surfaces you chose to calculate / display
4. The top surface is displayed (or surfaces if there are positive and negative maxima in your dataset). Positive values are displayed inn red-yellow and negative in shades of blue. Since these surface may be small it may be diffucult to see.
5. You can make more surfaces visible by pressing X or clicking the Threshold DOWN button on the side menu .. this effectively lowers your theshold by 10%
6. You can make fewer surfaces visible by pressing Y or clicking the Threshold Up button on the side menu .. this effectively raises your theshold by 10%
7. Press f or click the Cycle 3d button on the side menu to cycle through the following modes:

1. Positive and negative visible (default)
2. Positive only visible
3. Negative only visible
4. Neither visible
5. Back to positive and negative visible ... etc.

8. N.B. whilst cycling through, the threshold may be reset to highest values only, but this can be adjusted as required by pressing X / Y as described above

4. If you selected 2d-merged mode:

1. Prompts will tell you the maxima and minina that have been found in your data files .. if there are no negative values only one pop-up box is used for positive value choices (vica versa)
2. You will be asked to enter the lower boundary (or threshold) of the data to display. Enter the value and click OK. .. e.g. the maximum in your data might be 7.353 but you might only want to threshold the result at all values above 2.3 ( if loading z-stat data for example)
3. The default value in the pop-up box is 'skip'. This allows you to skip the generation of the positive values / negative values ( .. or both! .. ) so that positive or negative results can be viewed independently. Click OK without changing the value if you want to skip.
4. Give the program a few seconds to draw your results .. this can take up to a minute depending on the number of slices in your mri dataset
5. You can toggle between the original structural dataset loaded by pressing M or clicking the Switch 2d button on the side menu

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Loading - Dipoles (back to top)
Press D in the main window or select the dipole LOAD button on the menu to load dipole data file

> Information: Dipole data consists of a time-series with:

> > 3 x-y-z co-ordinates for the location of the centre of the estimated source
> > 3 x-y-z scalars describing the magnitude and orientation vector of the estimated source
> > 2 scalars describing the confidence and goodness-of-fit of the estimated source

After typing D in the main window or clicking the Load button under DIPOLE DATA on the side menu, you will be prompted to pick:

1. a 4D-Neuroimaging dipole overlay file – BROWSE, SELECT A FILE AND CLICK OPEN
2. a text file (any format) containing the 4x4 transformation matrix which described the values required to transform the MEG data set / space into the co-ordinate system of the currently loaded MRI set - BROWSE, SELECT A FILE AND CLICK OPEN YNIC Users: this file is generated for you when you use ynicBF to do a coregistration. It is usually saved for you in the same directory that contains you beamforming results (IMG_5mm and NAI_5mm) in your beamforming output path. It will be called something like home_andre_PhD_myexperiment_R1025b_c,rfDC_transform.txt.
3. Select the time-point for which you would like to display the initial dipole location e.g. you may be interested in the position of your dipole 100 ms after the start of your pre-defined epoch / data sample. – TYPE THE REQUIRED VALUE (in milliseconds) AND CLICK OK
4. Give the program a few seconds to load the data
5. The initial dipole position and orientation should be displayed. The radius of the sphere depicting the dipole source is proportional to the confidence in the localisation; the length of the orientation vector is proportional of the strength of the dipole
6. Hold down Ctrl and then click the left arrow ( ← ) or right arrow ( → ) cycle to the position of the dipole 1 ms previous in time or 1 ms forward in time respectively.
7. You can also change to colour of the dipole by picking it and changing the color (See CHANGING OBJECT COLOURS below)
8. Multiple dipole files can be loaded and displayed simultaneously, but when a new dipole data set is loaded the ability to interact with the previous set is lost.

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Loading a 3d brain surface (back to top)
If you have a generated cortical surface in Binary .OFF format, you can load it into your data.

> Information about the .OFF file fomat is available at http://www.geomview.org/docs/html/geomview_41.html#SEC44. A tutorial on generating your own will follow soon. A .off file example is provided in the examples directory (but is of course not guaranteed to co-register with your data!)

Press B in the main window or select the CORTICAL SURFACE LOAD button on the menu to load dipole data file
After typing B in the main window or clicking the Load button under CORTICAL SURFACE on the side menu, you will be prompted to pick:

1. a Binary .OFF file of the cortical surface – BROWSE, SELECT A FILE AND CLICK OPEN
2. Give the program a few seconds to draw your results .. this can take up to a minute depending on the resolution of your cortical surface file
3. Once the cortex is loaded it will appear as a red surface in the main window.
4. The surface can be toggles on / off by pressing v or by clicking the Visible On/Off button under CORTICAL SURFACE on the side menu
5. The surface can be faded in / out by pressing b / n respectively or by clicking the Opacity Up/Down buttons under CORTICAL SURFACE on the side menu

> > ADVANCED: Clicking V in the main window initiates the surface cutter. By clicking on and moving the spherical handles of each surface of the cutter cube, the surface can be sliced into in any plane. Click V in to turn the cutter off again. This procedure is pretty complex and calculation intensive so can be pretty slow.

Generating orthogonal plane views (back to top)

Key points: Before you start understand this: The ortho view window is in radiological format - unlike the main window which is neurological

You can generate orthogonal (in plane) views of you main window at any time, whatever type of data you are displaying.
Press x in the main window or select the ORTHO-VIEWS ON / UPDATE button on the side menu to create new views (these appear in a new pop-up window).
Make sure all the planes are visible by pressing C (coronal), A (axial) and S (sagittal) in the main window or selecting the corresponding button under MRI PLANES on the side menu.
If the views do not look correct, try pressing r in the main window or clicking the Reset button under MRI PLANES on the side menu. This will reset the current zoom.
Saving images out (back to top)
You can save images of your current view(s) to .tif files at any time. The image maker will save out the picture exactly as it appears on your screen and will ask you where and under what name you would like the file saved.
Press J in the main window or select the Main Window: save image button on the side menu to save the main window.
Press j in the main window or select the Ortho Views: save image button on the side menu to save the ortho window.
Snapping planes to a selected point (back to top)
You can make the x, y and z plane snap to any point on the image planes easily.
Simply hover your mouse pointer over the spot in the image you want the planes to intersect at and press o (lowercase letter o) in the main window.
Keyboard shortcuts (back to top)
Keyboard shortcuts can be called after clicking in the main window.
Keyboard functiona are cAsE seNsitiVE so make sure you use the right ones!

Main Window | r | Reset the zoom of the main window
o | Hover the mouse over a point and press the o key to centre all 3 planes on the point under the mouse pointer
L | Reset the 3 planes to the original orientation
C | Switch the coronal slice on / off
A | Switch the axial slice on / off
S | Switch the sagittal slice on / off
E | Switch the edges of the planes on / off
x | Create new / update current orthogonal views
j | Save the current orthogonal view to a tif file
J | Save the current main window view to a tif file
H | Cycle main window viewing angle
z | Turn help file on
q | Quit thye application (NB no confirmation)
Loading Data | F | Load functional data - Beamforming, fMRI or DTI Probability Distributions
D | Load dipole files
B | Load a brain - cortical surface
T | Load DTI fiber data
Beamforming / fMRI in 2d-merged mode | M | Switch between original structural image and functional data
Beamforming / fMRI in 3d isosurface mode | f | Cycle through visible surfaces: positive and negative (default) positive only negative only none
X | Make more surfaces visible ( lower threshold )
Y | Make fewer surfaces visible ( raise threshold )
Dipoles | d | Make the dipole visible / invisible
Ctrl <- | Show the dipole position 1ms earlier
Ctrl -> | Show the dipole position 1ms later
Cortex | v | Make the brain surface visible / invisible
V | Turn the surface cutter on / off
b | Fade the cortical surface out (more transparent)
n | Fade the corticla surface in (less transparent)
DTI | g | Make all loaded fibers visible
G | Hide all fibers
h | Make the region of interest selector visible
t | Place the region of interest selector at the point under the mouse pointer position
s | Place the mouseover the region of interest selector and press the s key to make all fibers passing through this area visible