delintenicolas/unravel

This repository contains the code of UtiliziNg tRActography to uncoVEr muLti-fixel microstructure (UNRAVEL).

unravel's Issues

RGB outputs

The way peaks_to_RGB() is written, increases the color dominance of fiber with high fiber volume fractions (fvf). Mulitplying by a sum a fiber volume fraction might create a better output.

Suggestion: change code to have two kinds of inputs color/peak modulators (fractions or fixelweights) and intensity modulators (FA or fvf).

Flesh out TIME documentation

Line only works when K=2

UNRAVEL/src/unravel/analysis.py

Line 49 in 293ad73

fixel_weights_roi = fixel_weights * np.repeat(roi[..., np.newaxis],

Adapt to make the line work with any number of fixel.

Nan in angle_difference

nan in angle_difference when two vectors are close to being similar due to arcos(>1)

if (v1n == v2n).all():
return 0
if (sum(v1nv2n))>1:
return 0
ang = np.arccos(sum(v1nv2n))*180/np.pi

Unify list/array output

get_weighted_sums, get_microstructure_map and total_segment_length all do similar operations and their input/ouput varies for the fixelWeight format.

coefList undefined when cfo=True in get_fixel_weights

coefList is undefined when cfo=True in get_fixel_weights

File ~\Anaconda3\envs\timeEnv\lib\site-packages\TIME\core.py:693 in get_fixel_weight
    for coef in coefList:

UnboundLocalError: local variable 'coefList' referenced before assignment

Improve get_micro_map flexibility

UNRAVEL/unravel/core.py

Line 1420 in 7545166

microMap += metricMap*fixelWeights[:, :, :, k]

Replace ":,:,:" by "[slice(None)]*len(dim)" to work with 2D arrays