Hi Sim,
When deciding which commands you need to use to make an ROI it is import to understand what type of image you are working with and in what space it is. For example, if you look at the Harvard-Oxford atlas image you can see that it contains values
everywhere in the brain, and therefore to isolate the brain region you are interested in you need to apply a threshold (to remove everything below a value using -thr and/or to remove everything above a value using -uthr). It is also important to make sure
that the resulting ROI image only contains 0s outsize the ROI and 1s inside the ROI, which is achieved by binarising using -bin. Lastly, the ROI image and the EPI image need to be in the same space before extracting the BOLD timeseries, so you may need to
use the applywarp command (followed by binarisation) to make sure your ROI image is in the right space.
You can find out more information about all of these by looking at the FSL wiki and usage information for commands.
Best wishes,
Janine
A further question: if I get a mask from others (it is not necessarily made using FSL), should I also use the command fslmaths, -thr, -bin to process it first before I use it?
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Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
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