Preproc-main into main#161
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Preprocessig script for outlier removal
preproc pipeline for brain
Test and simulation for brain denoising
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topup-eddy preproc script
…d the imports in /standardized
…ork with newer versions of python
Preproc main merge prep
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Is it needed to have a seperate file for the brain phantom for preprocessing? Can this not be combined with Oscar's digital brain phantom with additional "default" options for turning preprocessing-specific things on/off? This would make the code cleaner and phantoms more alligned
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The new file kind of looks better, it might make the existing one redundant. But I'm not sure. @ElinaPetersson ?
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Yes, sounds reasonable. I'll make one script with all functionality but optional relaxation decay.
oliverchampion
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oliverchampion
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With regards to the Matlab codes --> do we need to include all toolboxes like nifti_toolbox? This could make submits unnesicarily long. Also should check what the licensing is there; are we allowed to share that code? are we allowed to share it with out own license (typically licensing only allows sharing code with the same license).
The stuff that was submitted by ASD_MemorialSloanKettering? It's part of fitting code and has been in the repo for a while now |
merge to just one sim_brain_phantom script
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Fine to me once merge conflicts are resolved! |
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Describe the changes you have made in this PR
Added fitting and preprocessing folders to /src/original, with corresponding fixes to the imports in various files in the repository.
Added a line to pytest.ini to ignore files starting with "wip_*" during automatic testing.