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sct-pipeline / csa-atrophy

Evaluate the sensitivity of atrophy detection with SCT
https://csa-atrophy.readthedocs.io/
MIT License
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Resample images to desired resolution #85

Closed PaulBautin closed 3 years ago

PaulBautin commented 4 years ago

It was noticed in issue #83 that the CSA of rescaled t1w images was often overestimated. This could be caused by an increasing partial volume effect with tissue outside of the CSF. However, overestimation is less visible in t2w images, this is possibly due to better image resolution (0.8x0.8x0.8mm instead of 1x1x1mm). By resampling the T2w data to 1mm at the very beginning, it would be possible to see if difference between t1w and t2w results is caused by difference of native resolution.

DONE:

FIX #91

PaulBautin commented 3 years ago

I finally decided to implement issue #91 in this PR with commit https://github.com/sct-pipeline/csa-atrophy/pull/85/commits/6104cf5d9dd5b31b779ae55439d9ec5cb03861c7. @jcohenadad, i have tested this PR on a couple subjects and it works well. Could you review before merge?

PaulBautin commented 3 years ago

Last commits allow user to resample images to desired resolution. This new parameter must be configured in config_script.yml before running program.