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Inconsistent patch size from antspynet.extract_image_patches #46
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Oh, that's not good. Let me see if I can figure it out. |
Hey, @stnava , I just ran your code snippet a couple times on a couple different machines (2 macs/python 3.7 and archeozoic/python 3.8) and I'm getting patch shapes of the same size (20, 20). What are you getting? |
this should do it more reliably
you see things like: (20, 20, 13) I just ran this on archeozoic - images are in my ~/ |
were you able to reproduce? |
Sorry @stnava , just getting breakfast for the kids. I’ll test it in just a sec. |
np - am about to head out for surf in 4 degree weather |
Oh, man, that’s insane. |
Okay, yeah, I was able to reproduce. Interesting that it seems to be only in the 3rd dimension which makes me wonder if it is a dimensionality issue when I modified the code from 2-D to 3-D. I have to go run an errand (on my OneWheel so it'll kind of be like surfing but in 64 degree weather) but I'll work on it when I get back. |
Okay, check this commit which should fix the issue. |
that did it - thx! do you have any thoughts on my PR? |
Great. During my attempts at debugging, I found a second, unrelated bug so I'm glad you discovered this issue. I really didn't have any thoughts on the brain extraction part as I just assumed you had discovered a problem with "nobrainer". If its related to quality assessment than I confess I haven't used that much (although I was thinking quite a bit about these models recently with deep flash and using it to see if it is as I suspect that DeepFlash performs relatively better (compared to e.g., FreeSurfer) on higher quality data. |
Ok - I have several approaches to quality assessment
Important to note that outlierness , aesthetic quality versus noise versus
information scale and other things are all a piece of the puzzle
On Sat, Jan 15, 2022 at 6:24 PM Nick Tustison ***@***.***> wrote:
Great. During my attempts at debugging, I found a second, unrelated bug so
I'm glad you discovered this issue.
I really didn't have any thoughts on the brain extraction part as I just
assumed you had discovered a problem with "nobrainer". If its related to
quality assessment than I confess I haven't used that much (although I was
thinking quite a bit about these models recently with deep flash and using
it to see if it is as I suspect that DeepFlash performs relatively better
(compared to e.g., FreeSurfer) on higher quality data.
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brian
|
hi @ntustison - do you know a quick solution to this?
shows patches of variable sizes. when trying to compute consistent patch statistics, this can lead to issues of power. I believe this behavior is different from antsrnet.
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