README.md

Miscellaneous small scripts

• Inspect bvec to compare the quality of the approximate uniform spread with and without antipodal symmetry
• Fit DTI over multi-shell dataset to evaluate diffusivity for postmortem scan

Optimal b-value calculation helper scripts

These scripts work best on dataset with large number of different b-value

invMD_bmax.py
Produces helper maps to evaluate a choice of postmortem b-value

• DTI WLS fit over the full bvec/bval dataset and a mask
• returns various maps
  • mean diffusivity: MD
  • MD^-1
  • Fractional Anisotropy: FA
  • Inverse Largest eigenvalue: λ_max^-1
  • Maximum DTI signal contrast on last shell: ΔS = exp(-b_maxλ_min) - exp(-b_maxλ_max)

bvalue_estimator.py
Produces helper histograms to choose of postmortem b-value

• fit DTI WLS using all bvecs/bvals up to some b_max and iteratively increases b_max
• returns various metrics based on the MD distributions
  • Histograms of MD for each b_max
  • Graph of inverse histogram peaks as a function of b_max
  • Graph of inverse 50%-quantile of histogram as a function of b_max

deltaS_estimator.py
Produces helper histograms to choose of postmortem b-value

• fit DTI WLS using all bvecs/bvals up to some b_max and iteratively increases b_max
• returns various metrics based on the distributions of Maximum DTI signal contrast on last shell ΔS = exp(-b_maxλ_min) - exp(-b_maxλ_max)
  • Histograms of \Delta S for each b_max
  • Graph of inverse 25%- 50%- and 75%- quantile of histogram as a function of b_max

deltaS_estimator.py
Produces helper histograms to choose of postmortem b-value

• fit DTI WLS using each b-value shell
• returns various metrics based on the distributions of Maximum DTI signal contrast on shell ΔS = exp(-bλ_min) - exp(-bλ_max)
  • Histograms of \Delta S for each b-value
  • Graph of inverse 25%- 50%- and 75%- quantile of histogram as a function of b-value

TODO

List each script with more details
Give example call for each script
List dependencies for each scrip