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MICA-MNI / z-brains

z-brains: open software for brain lesion lateralization and localization
https://z-brains.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Clinical pdf #33

Closed rcruces closed 11 months ago

rcruces commented 11 months ago

Updates to the repo

  1. I edited the README, it looks prettier
  2. Added the ZBRAINS long logo
  3. Create the data directory with all the necessary surfaces for plotting and the png logo
  4. Created the functions/clinical_reports.py

Comments

  1. The multivariate analysis (mahalanobis) has a bug. I couldn't test its outputs: ADC-FA-flair-T1map-volume, ADC-FA-flair-qT1-thickness fails
  2. I recommend to use the string morphometry on the mahalanobis outputs instead of volume|thickness in all structures (hippocampus, cortex and subcortex). Keep everything else the same
  3. Note that there is only one value for cortical smooth 5mm, but is and optional variable in the function clinical_reports.py
  4. Note that there is only one value of hippocampal smooth 2mm, but is and optional variable in the function clinical_reports.py
  5. Check the permissions to write in the outdir
  6. All maps with the the string _threshold-* can be removed since this feature can be plotted within the function. I didn’t use them the thresholded data.
  7. Additionally I recommend to have only one variable thr for all the brain areas (cortex, subxortex and hippocampus). It is currently implemented like this
  8. I created a new directory under zbrains/data it contains the png logo and all the surfaces for plotting.
  9. The global variable zbrains MUST exist and is the path to the main repository <path_to/z-brains>

Other things

  1. Question: I suggest to remove all the 5k derived data, unless it is used for the SVM models, it does not look good for plotting.
  2. Question: Hippocampus why we have den=2 and 0p5 shall we remove one? The 0.5 den is way nicer. if this is used for SVM models the is ok.