fix the global normalization in bias field correction #387
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fix python-s in run_fastsurfer.sh (only use this if it is defined, else use python3.10 -- this is the default value and the in-docker fix to ignore user-space packages) fix bashrc definition in Docker/Dockerfile
rewrite/update N4_bias_correct.py - accept additional parameters (--aseg, --verbosity, --version) - port from optparse to argparse - change printing to logging facilities (instead of print), verbosity changes amount of prints. - rename functions and variables to follow PEP8 (lowercase, underscore to separate) - add function and integration to process the aseg and calculate wm intensity based on the wm segmentation from aseg - change normalization code to keep the zero-base (robust scaling should be done previously, e.g. typically in conforming) - rearrange code structure so functions are not as dependent on flags. Specifically, whether or not specific flags/files are present is moved to the main script. Consequently, functions are more predictable and not dependent on arguments.
m-reuter
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Nov 9, 2023
m-reuter
reviewed
Nov 9, 2023
fix doc string talairach origin
dkuegler
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@m-reuter The call to N4_bias_correct was in fact wrong. So, unfortunate... It is going to delay any new release... |
change the renormalization (--skipwm mode) to only consider the average intensity of the masked image. fix docstring in image_io.py
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To address incorrect etiv estimates, several changes to the bias field estimation and the pipeline are implemented
Addresses #378 .