Fixing brain phantom values #465
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…006a) Introducing Reproducibility notes into `brain_phantom2D`
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## master #465 +/- ##
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- Coverage 90.94% 87.03% -3.91%
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Brainweb is already referenced in the documentation:
Creates a three-dimentional brain Phantom struct. Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 mm.
References
B. Aubert-Broche, D.L. Collins, A.C. Evans: "A new improved version of the realistic digital brain phantom" NeuroImage, in review - 2006 B. Aubert-Broche, M. Griffin, G.B. Pike, A.C. Evans and D.L. Collins: "20 new digital brain phantoms for creation of validation image data bases" IEEE TMI, in review - 2006 https://brainweb.bic.mni.mcgill.ca/brainweb
These are the parameters I used (Aubert-Broche, B. et al., 2006a)
https://github.com/JuliaHealth/KomaMRI.jl/blob/v0.1-alpha/src/data/Brain2DParameters.png
The 00 for the muscle must be a typo in the table. The skin value I could have changed on purpose (see JEMRIS's brain phantom).
Please check that phantom3D also has these changes.
KomaMRIBase/src/datatypes/Phantom.jl
Outdated
| - Aubert-Broche, B., Alan C. Evans, and Louis Collins. | ||
| "A new improved version of the realistic digital brain phantom." NeuroImage 32, no. 1 (2006): 138-145. (Aubert-Broche, B. et al., 2006a) | ||
| - Aubert-Broche, B., Mark Griffin, G. Bruce Pike, Alan C. Evans, and D. Louis Collins. | ||
| "Twenty new digital brain phantoms for creation of validation image data bases." IEEE transactions on medical imaging 25, no. 11 (2006): 1410-1416. (Aubert-Broche, B. et al., 2006b) | ||
| - https://brainweb.bic.mni.mcgill.ca/brainweb/tissue_mr_parameters.txt (BrainWeb) | ||
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| ## Reproducibility notes | ||
| - T1, T2, T2* and PD Values for CSF, GM, WM, FAT, MUSCLE, SKIN/MUSCLE, SKULL, VESSELS, FAT2, DURA, MARROW are extracted from (Aubert-Broche, B. et al., 2006a) | ||
| - The T1 value for muscle is extracted from (Brainweb) as (Aubert-Broche, B. et al., 2006a) reports a 00 value. | ||
| - The T1 value of SKIN/MUSCLE is different between (BrainWeb) and (Aubert-Broche, B. et al., 2006a), we used the latter one. |
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Remove "Reproducibilty notes". Do not modify previous citations; just add more specific link to brainweb parameters.
Including required changes.
This PR is to fix #464