I have MRI T2 weighed images and need to create a mask to remove skull and others. I have a total of 30 MRI models and need ultimately need to measure infarct volume percentage. I also need to do spatial normalization. How to do this as if I’ve never used 3d slicer (true).
There are lots of neuroimaging tools you can use to do things that - I’m not sure Slicer is the best for doing a batch of 30 cases since it’s more geared for interactive use where others can be used from a script or command line. When you say infarct I guess you mean stroke and I don’t think we have an extension for that, but I’ll bet something exists out there outside of Slicer if you do a literature search.
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Hi Steve,
Ok. Would ITK-snap be a better option to do this? Or which neuroimaging tool would you recommend?
Thanks,
Joe
Not ITKSnap, something more like FSL or a tool in the freesurfer suite. I’m not familiar with a specific tool for stroke, but there must be something out there.