Mrgrid crop change intensity values of images

Hello, I’ve used mrgrid to extract several patches from the hippocamppus. I normalized the brain images before cropping them, now the patches that I extracted are in different intensity values as you can see in this image (in red the patch intensity range, both images are same brain with two different patches):

Do you have any idea why is that happening? how could I keep the same intensity range as the brain where the patches come from?



Hi @Al-yhuwert,

I’m not hugely familiar with FSLview, but it seems to me like the underlay image is not displayed with the same scaling as the overlay patch? You need to ensure the min & max values are the same for all images before concluding that there is any difference in scaling.

Alternatively, you should be able to read the intensity value at the position of the crosshairs for both images. That should hopefully show the same value for both images.

If this still doesn’t check out, we can look into it more closely – maybe you could send us the data and the extracted patch, and we can investigate from there.

All the best,

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Thank you @jdtournier!

Yes, the intensity value at the position of the crosshairs for both images is the same, thanks.
I was looking at the wrong place. :person_facepalming:

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