Hi folks,

has someone an idea or an advice to label two or three 4D (3D MRT + time ) objects coming out of the WEKA segmentation in the so called possibility map? I already tried a few options I read in this forum but didnt’t get any good results. They are MRT niftis of lymph nodes from which I want to analyze their signal intensity over time after I segmentated them in Weka.

And further question: Are there any Plugins which I could use to analyze these objects or 3D ROIs over time without swtiching to a program as matlab?

Morning

Perhaps the 3D Objects Counter plugin is what you are looking for:

Thank you for your advice @Danielle_Z

Unfortunately all label processes we tested in Fiji ended up in loosing the time dimension.

We tried to bypass this problem with multiplying the binary mask we got out of this process (without the time dimension) with the original probability mask (with time dimension). But, again, Fiji doesn’t allow us to multiply because you cant multiply different dimension files, of course. So now our problem is how we can make a “repmat”-function known from matlab with our 3D mask data:

new(x,y,z,t) = repmat(orig(x,y,z),[1 1 1 t]) is the matlab command.

So we want to make a 3D file with n copies of itself to make a huge 3D Stack which we than can transform in a 4D Hyperstack…and then finally could multiply with the 4D probability map for a clean mask which respect the time frames…

I know it sounds very difficult, but we couldn’t find an easier way. Very, very much thanks in advance if somebody could help us!