# How to create a brain mask from MRI T2 (30 MRI total)

**URL:** <https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338>\
**Category:** Support\
**Tags:** mri, brain, masking\
**Created:** [September 11, 2024, 9:54pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338 "2024-09-11T21:54:47Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![jegiron](https://avatars.discourse-cdn.com/v4/letter/j/6f9a4e/32.png) [@jegiron](https://discourse.slicer.org/u/jegiron)\
**Post date:** [September 11, 2024, 9:54pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338/1 "2024-09-11T21:54:47Z")

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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).

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [September 12, 2024, 12:30am UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338/2 "2024-09-12T00:30:08Z")

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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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**Author:** ![jegiron](https://avatars.discourse-cdn.com/v4/letter/j/6f9a4e/32.png) [@jegiron](https://discourse.slicer.org/u/jegiron)\
**Post date:** [September 13, 2024, 7:28pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338/3 "2024-09-13T19:28:07Z")

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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

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [September 13, 2024, 7:36pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338/4 "2024-09-13T19:36:55Z")

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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.