Dear FSL experts,
I know that the index number in xml file are one less of index number in maxprob atlases (e.g. in HarvardOxford xml the frontal pole has index 0, but within the atlas HarvardOxford-maxprob it has intensity number 1) and, nevertheless, this implies there is a correspondence between indexes and intensities; but, they are not the same things: intensities are probabilities and indexes are labels. In fact, when I open HarvardOxford-maxprob-thr0-1mm with FSLView and search the frontal lobe with atlas inspector tools I found intensity 1 (is correct), but just I select the option "Preview selected structure's probability map", it becomes 76. So, my query is this: when I have to mask specific region (e.g. frontal pole in HarvardOxford) with the command fslmaths, do I have to use the "-thr" argument with the number 1 or the number 76, or other specification to be sure I have selected my specific region?
I hope is clear.
Thanks in advance
AAV
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