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processing_stream_-_flatmaps [2011/04/03 04:19] (current)
jochen created
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 +====== Flatmaps ======
 +===== Motivation =====
 +While [[Processing stream - surface projection|surface projection]] of results already makes a much larger amount of cortical activation visible "at a glance"​ (compared to showing single slices, for instance), it still requires at least two separate images for the lateral and medial portion of cortex (for one hemisphere).
 +One way to circumvent this problem is by producing what people in the field have coined "​flatmaps"​. As part of the processing, the surfaces are first hugely inflated, then "cut open" (kind of like the peel of an orange; usually with a small patch of surface being removed entirely to minimize later distortion) followed by flattening the remaining vertices into a two-dimensional plane (which usually includes some kind of distortion correction, given the high amount of deformation this procedure introduces).
 +The result usually looks something like this:
 +{{:​neuroelf_gui:​flatmap_lh_sample.jpg?​840x680|Example of a flatmap, left hemisphere}}
 +===== Requirements =====
 +To create flatmaps such as the one shown above you need
 +  * a statistical map you want to visualize (can already be in [[xff - SMP format|SMP format]], otherwise [[xff - VMP format|VMP]])
 +  * the surface file representing the folded hemisphere (structure, used to sample statistical or functional data)
 +  * a flattened version of the surface file with identical number of vertices and neighborhood information (vertex inter-connectivity)
 +In case you do not have a surface file of your own, you can use the surface files created during a call to [[neuroelf_makefiles]] which are a representation of the single-subject brain used in SPM, Colin_27 (the 163,​842-vertices version of the left hemisphere of this dataset was used to create the above screenshot).
 +===== Procedure =====
 +Two paths are described below: sampling existing statistical information (in [[xff - VMP format|VMP format]]) at the spatial location of folded cortex and displaying it as a flatmap **or** sampling timecourse information and creating statistics (currently only implemented in BrainVoyager QX!) and then using the required [[xff - SRF format|SRF]] and [[xff - SMP format|SMP]] objects from BrainVoyager in NeuroElf for a high-quality screenshot.
 +==== VMP-based ====
 +If you have a VMP with one (or sevaral) map(s) you wish to visualize as a flatmap
 +  * load and select the VMP in NeuroElf GUI (either by using the File -> Open file request dialog or by issuing ''​vmp.Browse;''​ on the VMP object variable)
 +  * load and select the desired **folded** surface you wish to use for sampling the statistical data into surface-space (again either by using File -> Open or ''​srf.Browse;''​)
 +  * select the ''​**Create SMP...**''​ entry from the [[NeuroElf GUI - menu tree#​vmp_menu|VMP menu]]
 +  * optionally store the created SMP (e.g. for later use in NeuroElf or BrainVoyager QX)
 +  * ensure that the shown map is correctly displayed (activations should be on the correct hemisphere and in the right orientation!)
 +  * load and select the corresponding **flattened** surface (which must share the number of vertices and neighborhood information!)
 +  * if required, select the newly created SMP for this flattened surface, then select the desired map (if multiple maps are available)
 +  * click the "​undock"​ button of the main UI (top button in the [[NeuroElf GUI#​view_page_selection|View/​Page selection toolbar]])
 +  * use the **//SHIFT +// S** [[NeuroElf GUI - keyboard commands#​satellite_ui|keyboard command]] to invoke the screenshot function
 +  * select **Encapsulated PostScript (*.eps)** as file format
 +  * save the file
 +  * open (or switch to) a graphics editing program (such as Adobe Photoshop or The GIMP)
 +  * open the saved file and select a high-enough resolution (at least 300DPI) and the desired color space (RGB or CMYK) for rendering
 +  * optionally re-touch the image (for the screenshot above, the black background was replaced with a white background, leaving a small black fringe/​border using the magic-wand-tool)
 +  * save the image to a different format (rendered, bitmap)
 +==== MTC/​SRF-based ====
 +This is only required in case you wish to use NeuroElf for saving surface screenshots in EPS format!
 +  * use BrainVoyager to compute the statistics in SMP format (see BrainVoyager manuals for help)
 +  * save the SMP
 +  * load the flattened surface (SRF) and corresponding SMP in NeuroElf
 +  * continue with the above list of instructions starting with the "​undock"​ button instruction
processing_stream_-_flatmaps.txt ยท Last modified: 2011/04/03 04:19 by jochen