Vviewer is a light-weight viewer for MR data. Currently, we support .nii, .nii.gz, .img/.hdr and .v (lipsia's vista format). The viewer is written in python and does not have any external dependencies.
Vviewer is a light-weight viewer for MR data. The idea is to keep the viewer fast and simple, yet powerful. The viewer also features many practical keyboard shortcuts.
You can find the installation ...
Currently, the following file formats are supported:
*.nii,
*.nii.gz,
*.img/.hdr and
*.v (lipsia's vista format)
The viewer is written in python and does not have any external dependencies.
#Usage
You can find the installation ... ???
#How-to
## Open an image
You can open images directly from the terminal, using
vviewer.py -in data.nii
Alternatively, you can click in the menu on file / open image.
Alternatively, you can click in the menu on file / open image or hit "o".
## Clicking and slicing
The viewer shows three panes: coronal, saggital and axial. You can click and drag into any of the panes to navigate within the given plane. You can use the arrow keys on your keyboard to navigate in a voxel-by-voxel fashion (the green crosshair indicates the active pane).
The viewer shows three panes: coronal, saggital and axial. You can click and drag into any of the panes to navigate within the that plane. You can use the arrow keys on your keyboard for voxel-by-voxel steering (the green crosshair indicates the active pane).
In order to zoom into the image, use your mouse wheel or "," and "." on your keyboard.
If you want to shift the image left, right, up or down, hold the mouse wheel button while moving.
If you want to pan the image left, right, up or down, hold the mouse wheel button while moving.
The voxel's current location is displayed in the ???, in voxel coordinates. If you want to switch to millimetres/MNI coordinates, click on the button???. The intensity value of the current image at the crosshair's position is shown ???.
## Multiple images and overlay
You can display multiple images simultaneously, overlaid on each others. The order of the images can be changed with the two buttons ???. The most top image is also drawn on top all other ones. If you want to turn an image invisible, click on the checkmark ??? next to the image name. Vviewer shows you the values for the crosshair voxel for all images (with "a:" denoting the most top image, "b:" the one below, etc.)
You can overlay multiple images on top of each others. The order of the images can be changed with the two buttons ???. The most top image is drawn on top all other ones. Shift their order with the arrow buttons next???. If you want to turn an image invisible, click on the checkmark ??? next to the image name. Vviewer shows you the values for the crosshair voxel for all images (with "a:" denoting the most top image, "b:" the one below, etc.)
## Colormap
## Colormaps
### Basics
Images are displayed by a means of a colormap, which assigns a color to given values in the image. Per default, this is a gray-scale colormap, assigning black to the smallest value in your image and white to the largest. You can however manipulate the ending points of the color mapping with the slider ???. Pulling down the upper handle will change the value that is rendered as white. This value is shown ???. For instance, instead of drawing the maximum value of 500 as white, you may pull the upper handle to a value of 250. Thus, the value of 250 will be shown as white, and all values above 250 will also be shown as white (per default, this behaviour can be changed). Thus, the overall brightness of the image increases. Similarly, if you manipulate the lower handle of the slider, the value assigned to black is changed. It is shown ???. For instance, pulling the value from 0 to 100 means that the value 100 is now assigned to black. However, values below 100 are not drawn anymore and are invisible. This behaviour can be changed, see ???.
### Change the color map
You can change the colormap and select another one by clicking on the color map.
Images are displayed by a means of a colormap, which assigns a color to the given values. By default, we use a gray-scale colormap, assigning black to the smallest value in your image and white to the largest, everything in between will be a shade of gray. You can manipulate the color mapping with the slider ???: pulling down the upper handle will change maximum value which is shown in *white*. The given maximum value for white is shown ???. For example, let us say that the default maximum value for white is 500 (because it is the maximum in your image). Now, instead of drawing the value 500 as white, you may pull the upper handle to 250. Thus, the value 250 will be shown as white, and all values above 250 will also be shown as white too (per default, this behaviour can be changed, see clipping behaviour later). Effectively, the overall brightness of the image increases, as the middle gray color now will be shown for a value of 125 (instead of 250 as before). Similarly, if you pull the lower handle of the slider, the value assigned to *black* is changed ??? lower handle. For instance, pulling the value from 0 to 100 means that the value 100 is now assigned to black. Values below 100 are *not drawn* anymore and are *invisible*. This behaviour can be changed, see clipping behaviour.
### Different color maps
You can change the colormap and select another one by clicking on the color map. We have a selection of colormaps ready to select. Feel free to request another one here on git if you don't find your favourite one. Note that the color for the maximum value is displayed on the right side of the color bar, while the minimum is shown on the left.
### Two color maps
If you want to display positive and negative values with different colors, you can activate a second color bar. Just press "i" or go to image/image settings, and this will bring up the image menu. There, select "color maps" and "two color maps".
The second color map has its own sliders, which are shown to the right of the first one, allowing to set independent thresholds.
Some situations require that you want to have two color maps for the same image. For instance, if you want to display positive and negative values with different colors. You can activate a second color bar for such situatinos, just press "i" or go to image/image settings. This will bring up the image menu. There, select "color maps" and "two color maps".
Alternatively, you can open the image directly with the *-z* flag:
vviewer.py -z data.nii
### Clipping behaviour
What happens to values that are outside the range of the color map assignment? Per default, values ABOVE the upper limit are shown in the same color as the maximum for the color map. Values BELOW the lower limit are however not drawn and are invisible. We call this procedure "clipping". You can change the default behaviour in the image settings menu (press "i"), clicking the checkboxes regarding clipping.
The second color map is independent of the first one and has its own slider with maximum and minimum handle. They are shown to the right of the first one.
### Clipping behaviour
What happens if the image values are outside the range of the color map assignment? Per default, values *above* the upper limit are shown in the same color as the maximum. Values *below* the lower limit are however not drawn and thus invisible. We call the latter procedure *clipping*, meaning that colors are just clipped away. You can change the default behaviour in the image settings menu (press "i") or image/image settings. There, for each active colorbar you find two checkboxes for clipping. By default, the "clip upper threshold" for the positive colorbar is disabled (meaning that values above are just shown with the maximum color) and "clip lower threshold" is enabled (making them invisible if below).
change Colorma
have two colormaps. sliders!
clipping properties
## Histogram
tools /histogram of "h"
linkage to the sliders
moving, shifting!
You can show the histogram of values for the currently selected image via tools/histogram or by pressing "h". On the x-axis, you will find the given image values, on the y axis the count. The section of image values that is within the selected colormap is shown in blue, meaning that if you pull the colormap handles, this box will shift. You can however also directly interact with this box, resulting in changes in the colormap. You can also move around the whole range by dragging the blue box. This can be useful for looking for a band of image values (with enabling clipping on both sides).
## Time series data
slider for Time
n and b and space
t or image/image time series
The viewer is able to load time series data. If time series data is detected, the area ??? becomes active for the user. The number box shows the currently selected time volume, here you can enter a number to jump to the volume directly. The horizontal slider shows the position in the overall time series. You can drag it to show the time series data at any given point. If you want to move in time in a more controlled fashion, you can click the buttons??? to just move one volume forward or back. The same can be achieved by pressing "n" and "b" (next and before). Clicking the play button ??? will play the time series back to you. You can also start/stop it by hitting "space".
## Maximum and minimum
You can jump to the local maximum or minimum of the selected image. For this, click on the buttons ???. The search radius can be changed in the preferences.
# Advanced stuff
# Advanced
## Mosaicing
You can create a mosaic view of the currently selected images and thresholds. For this, click on Tools/Open Mosaic Dialogue or hit "m". ???direction??? You can determine the grid of the mosaic by setting the numbers of rows and columns, which determines the number of slices. The starting frame and end frame set the slice end points. If the slices are perfectly divisible the *increment* field shown on the bottom will be in bold. Having the increment in bold ensures that the slice distance is the same within the mosaic. Hit "slice to mosaic" to render it. Note that in the mosaic you will still be able to zoom and pan.
## Colormap Clipping
## bring window out. link views
## linked views
## Resampling options
Images usually come with affine transformations (saved in the header), that encode a translation and rotation. You can disable the resampling and sample to the next closest voxel resolution by clicking on Resampling/Ignore affine and pray.
##
#Keyboard shortcut cheat sheet
* o: open file
* cursor left,right,up,down: change crosshair position within selected pane (green one!)
* page up/down: change voxel position in remaining dimension (orthogonal to the selected plane)
* h: histogram
* m: mosaic dialogue
* v: toggle image visibility
* space: start/stop playing movie for time series
* n/b: move to next or previous frame in time series
