====== Image montage UI ======

===== Motivation =====
While for data inspection the screen resolution (e.g. 1mm equals one pixel for the 3-slices view) is sufficient, paper-based publication (articles, posters, etc.) usually require much higher resolution images (e.g. at least 150 dpi, which means that for those pictures, a super-sampling of at least factor 6 is required to get 25.4 * 6 = 152.4 pixels into one inch!).

As the main UI does not allow that kind of high-resolution zoom, a different UI is available for this task.

===== Layout =====
The image montage UI is available via the Visualization -> Create montage images menu item and looks like this:

{{:neuroelf_gui:montageconfig.png|NeuroElf - montage image configuration}}

This dialog has the following controls and properties:
  * slicing direction (supports sagittal, coronal, and axial/transversal)
  * flipping of slicing direction (non-flipped: ''min:step:max'', flipped: ''max:-step:min'')
  * X-flip (for coronal/axial slicing, flip along dataset's X axes, orientation)
  * X/Y/Z coordinate range (set minimum value and step to 'S' for single slice image)
  * super-sampling factor (up to 8)
  * montage packing layout (default: letter formatted output)
  * re-setting background color (replacing black with a color, incl. smoothed border support)
  * adding up to 10 pixels of additional border between images
  * either show output or write to file (using ''imwrite'', different formats supported)
  * pre-defined volumes to cover the brain of different template spaces

===== Configuration example =====
This is a typical usage example. Make sure to configure the statistical map(s) with the correct threshold (stat, k), colors, etc!

  * for the MNI brain, the drop-down can be set to ''MNI brain'', which then sets
    * X, Y, and Z min/max to -78/78, -110/82, -64/92
    * using the configured step-size to determine number of slices
    * sets a new default layout (and updates the layout dropdown choices)
  * enabling X-flip
  * choosing a step-size of ''3'' sets the layout default option to ''6 x 9''
  * setting the super-sampling factor to 4
  * enabling anatomical transparency
  * choosing a new background color R: 40, G: 100, B: 160 (middle-light blue)
  * adding 6 pixels of border
  * choosing ''Show in figure''
  * disabling (if necessary) ''Display during slicing'' option
  * click on ''Create montage...''

The output then looks like this (for a random covariate thresholded with r >= 0.275)

{{:neuroelf_gui:montage_example.jpg|Montage example}}

And a zoomed snippet (using Matlab's internal zoom/lens button) reveals the sub-millimeter resolution and the shaded transparency of the border:

{{:neuroelf_gui:montage_example_zoomed.png|Montage example zoomed (cropped)}}