processing_stream_-_flatmaps
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— | processing_stream_-_flatmaps [2011/04/03 02:19] (current) – created jochen | ||
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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" | ||
+ | |||
+ | One way to circumvent this problem is by producing what people in the field have coined " | ||
+ | |||
+ | The result usually looks something like this: | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ===== 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, | ||
+ | |||
+ | ===== 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 '' | ||
+ | * 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 '' | ||
+ | * select the '' | ||
+ | * 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 " | ||
+ | * use the **//SHIFT +// S** [[NeuroElf GUI - keyboard commands# | ||
+ | * 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/ | ||
+ | * save the image to a different format (rendered, bitmap) | ||
+ | |||
+ | ==== MTC/ | ||
+ | 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 " | ||
processing_stream_-_flatmaps.txt · Last modified: 2011/04/03 02:19 by jochen