3D (stack) mask

[Eric BADEL-2]

Hi all,
I'm working with 3D solumes (stacks). After threshold of all slices, I
need to work on one volume ROI. For that, I need to create a selection
or a mask that corresponds to the thesholded area on each slice. then, I
should apply this mask to my whole stack.
Actually, using the threshold image, if I just perform a "create mask"
or "create selection", ImageJ just deals with the current slice.
Do you know something that could help ? Something like "3D mask"  ?-)
Thank you.
Eric

[michele_casanova]

Hey Eric,

I found how to do it... (it is probably not helpful for you after 3 years but let's write it for the next users :) ).

If you have a dataset with the grey-scale image and a dataset (mask) which is a binary image only with 0 and 1 values, you can apply the 3D mask to your image by using the image calculator:

Process - > Image Calculator -> select your image as image1 and your mask as image2, and select "Multiply" as the operation -> OK

Be careful though: your mask should have only pixels with 0 or 1 as values... otherwise you will not extrapolate the mask correctly!

Hope it helps,

Cheers,

Michele

--
Michele Casanova, PhD candidate
MSc ETHZ ME
Institute for Biomechanics
HCI E 451
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