Hello,
If I choose a 2 voxel neighbourhood size, does that equate to a ROI of 5x5x5?
Andrew
it depends on the voxle size of your data - if its 2mm^3 then a 2 voxel neighborhood would be a 4mm ROI
it depends on the voxle size of your data - if its 2mm^3 then a 2 voxel neighborhood would be a 4mm ROI
Sorry, i mispoke. You can get an idea of the number of voxels in a neighborhood from the GUI. I don't have access to matlab to guide you specifically today, but Nancy or I can do it Monday.
From Section 7.1.2 of the online help:
You can use average intensity of the neighborhood voxels for intensity of the clicked voxel by specifying Neighborhood Size field (An edit box in Voxel Intensity Plot window). By default, it is 0, which means no neighborhood voxel is included. Otherwise, neighborhood size represents the distance (number of voxels) from the clicked voxel. In this case, the average intensity will include those voxels:
Do not set neighborhood size unnecessary large, because the maximum number of neighborhood voxels is equal to the cubic of� (SIZE * 2 + 1). e.g. Neighborhood Size 1 could have a neighborhood of 27, and Neighborhood Size 3 could have a neighborhood of 343, etc.
from 7.1.3:
Click Multiple Voxels Extraction under Windows menu, and select the above voxel location file. Input only a prefix of the extracted file name, and you will be prompted to select a voxel neighborhood size to use average intensity of the neighborhood voxels for intensity of the selected voxels in your location file. It works the same way as the neighborhood voxels we discussed above. Click OK button, it will generate two kinds of files:
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So, to answer your question, you need to go back into the "voxel response/response function plot" and select each of your coordinates with the chosen neighbour size". If a neighbour of 1 provides enough smoothing to give you a realistic representation of the effect in that region, use that. I wouldn't suggest going much higher than 2. Use the reported # voxels in the neighborhood to report the volume over which you are averaging. If you play around with the BSR plot at all, you will need to replot it to have the revised voxel count show up in the "voxel response" window (depending on the module you're using)
cheers
Nancy
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