MULTI_SHELL_Estimate

MULTI_SHELL Estimate

Command:

dmriprep

Module version:

0.1

Module type:

prep

Attributes:

utility, identity

Notes:

MULTI_SHELL_Estimate README

Source:

dtiplayground/dmri/preprocessing/modules/MULTI_SHELL_Estimate

Global variables

Values this module shares with the other modules of the pipeline (dmriprep run -g <name>=<value> sets one).

  • dti_path

Protocol options

tool

Tools to estimate multi-shell models (dipy / AMICO NODDI / mrtrix3)

Type:

list

Default:

dipy

Choices:

  • dipy – Use DIPY library

  • amico – NODDI model of AMICO (NDI, ODI, FWF)

  • mrtrix3 – mrtrix3 dwi2adc (S0, ADC)

model

Model

Type:

list

Default:

dti

Used when:

tool is dipy

Choices:

  • dti – Diffusion Tensor

  • dki – Diffusion Kurtosis (tensor, FA/MD/AD/RD, MK/AK/RK/MKT/KFA, kurtosis tensor)

  • msdki – Mean Signal Diffusion Kurtosis (MSD, MSK)

  • fwdti – Free Water Elimination Diffusion

  • ivim – Intravoxel Incoherent Motion

optimizationMethod_dti

Optimizaition Method

Type:

list

Default:

wls

Used when:

model is dti, tool is dipy,amico

Choices:

  • wls – Weighted Least Squares

  • lls – Linear Least Squares

  • nls – Non-Linear Least Squares

  • ols – Ordinary Least Squares

  • restore – RESTORE

optimizationMethod_fwdti

Optimization Method

Type:

list

Default:

nls

Used when:

model is fwdti, tool is dipy

Choices:

  • wls – Weighted Least Squares

  • nls – Non-linear Least Square

optimizationMethod_dki

Optimization Method

Type:

list

Default:

wls

Used when:

model is dki,msdki, tool is dipy

Choices:

  • wls – Weighted Least Squares

  • ols – Ordinary Least Squares

  • nls – Non-linear Least Square

split_b_D

The b-value to split the data on for two-stage fit. This will be used while estimating the value of D

Type:

float

Default:

400

Used when:

model is ivim, tool is dipy

split_b_S0

The b-value to split the data on for two-stage fit. This will be used while estimating the value of S0

Type:

float

Default:

200

Used when:

model is ivim, tool is dipy

maskPath

Brain mask (NRRD or NIfTI); if empty, the mask of BRAIN_Mask is used, else the whole image

Type:

filepath-remote

Default:

not set

Used when:

tool is dipy,amico