Crop around transformed segmentation

sct-pipeline / csa-atrophy

Evaluate the sensitivity of atrophy detection with SCT

https://csa-atrophy.readthedocs.io/

MIT License

1 stars 0 forks source link

Crop around transformed segmentation #89

Closed PaulBautin closed 4 years ago

PaulBautin commented 4 years ago

This PR aims to implement: https://github.com/sct-pipeline/csa-atrophy/issues/88#issuecomment-716824280. Up to know cropping was performed around a dilated initial segmentation. The new method transforms initial segmentation before cropping image, this ensures spinal cord does not exceed image boundaries.

DONE:

transform and dilate the labelled segmentation to crop image
update csa_rescale_stat.py, extract the "rescale" from updated "Filename"

FIX #88

jcohenadad commented 4 years ago

@PaulBautin is it ready for review?

PaulBautin commented 4 years ago

Yes, it was tested on a 2 subjects that caused issues in precedent runs.

PaulBautin commented 4 years ago

@jcohenadad, could you have a look when you find the time?

jcohenadad commented 4 years ago

@PaulBautin i'm looking into that now

Yes, it was tested on a 2 subjects that caused issues in precedent runs.

can you pls specify the 2 subjects you are talking about? i'm trying to reproduce

EDIT 2020-10-30 16:59:15: Nevermind, I found the problematic subject and confirm that your new implementation solves that problem 👍