Feature/b0restore

[jchen33344]

New outlier correction: -b0restore

• Outlier voxels show flatter spherical mean slopes at low b-values, so this is an iterative correction method that adjusts outlier voxel’s b=0 signal using neighboring voxels’ (5x5x5 patch) log signal decay slope/rate (between b=0 signal and spherical mean signal of b=1000 shell).
• Outliers in the first iteration are detected using the same method as -akc_outliers, where the kurtosis tensor is projected onto a sphere with 256 directions and voxels where mean kurtosis is less than 0 (-2 for 2nd iteration and beyonf) or greater than 10 are labeled as outliers. Plus, any voxels with RK < 0.5 (excluding CSF) are considered outliers as well.
• Use -akc_lowerlim <default="0"> and akc_upperlim <default=10> to set your own lower and upper AKC limit, respectively.
• Neighboring voxels are selected as the top 10 percent of voxels (may be adjusted using -percentile <default=10>) within a 5x5x5 patch (-kernal <default=5>) with the most similar voxels using Euclidean distance of signals.
• b=0 signals in outlier voxels are iteratively corrected until outlier reduction is <5% -thresh_criteria <default=0.05>

Using -b0restore will also output:
-'outliermask_final_dki.nii' : Final outlier mask after b0-restore
-'dt_dki_b0restore.nii' : dt after b0-restore
-'b0_dki.nii' : final b=0 images after b0-restore
-'b0_indices.txt' : volume indices for b0s

[jchen33344]

example usage:

path=/workspaces/DESIGNER-v2/m0033

tmi -DKI -WDKI \
-akc_lowerlim 0 -akc_upperlim 10 \
-mask $path/brain_mask.nii -b0restore -kernal 5 -percentile 10 \
"$path/dwi designer.mif" $path/params