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neuroelf_gui_-_image_montage_ui [2010/06/15 06:16] (current)
jochen created
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 +====== 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)}}
neuroelf_gui_-_image_montage_ui.txt ยท Last modified: 2010/06/15 06:16 by jochen