reconst_dtimetrics

Script to compute all of the Diffusion Tensor Imaging (DTI) metrics

Keywords : nifti, DTI, tensor, scilpy

---

Inputs

Input 1

Format : tuple val(meta), path(dwi), path(bval), path(bvec), path(b0mask)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
dwi	file	Nifti DWI volume used to extract DTI metrics.	True	*.{nii,nii.gz}
bval	file	B-values in FSL format.	True	*.bval
bvec	file	B-vectors in FSL format.	True	*.bvec
b0mask	file	Nifti b0 volume file used to mask the input image.	False	*.{nii,nii.gz}

---

Outputs

ad

Format : tuple val(meta), path(*__ad.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__ad.nii.gz	file	Axial diffusivity.	True	*__ad.{nii,nii.gz}

evecs

Format : tuple val(meta), path(*__evecs.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evecs.nii.gz	file	Eigenvectors of the tensor.	True	*__evecs.{nii,nii.gz}

evecs_v1

Format : tuple val(meta), path(*__evecs_v1.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evecs_v1.nii.gz	file	First eigenvector.	True	*__evecs_v1.{nii,nii.gz}

evecs_v2

Format : tuple val(meta), path(*__evecs_v2.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evecs_v2.nii.gz	file	Second eigenvector.	True	*__evecs_v2.{nii,nii.gz}

evecs_v3

Format : tuple val(meta), path(*__evecs_v3.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evecs_v3.nii.gz	file	Third eigenvector.	True	*__evecs_v3.{nii,nii.gz}

evals

Format : tuple val(meta), path(*__evals.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evals.nii.gz	file	Eigenvalues of the tensor.	True	*__evals.{nii,nii.gz}

evals_e1

Format : tuple val(meta), path(*__evals_e1.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evals_e1.nii.gz	file	First eigenvalue.	True	*__evals_e1.{nii,nii.gz}

evals_e2

Format : tuple val(meta), path(*__evals_e2.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evals_e2.nii.gz	file	Second eigenvalue.	True	*__evals_e2.{nii,nii.gz}

evals_e3

Format : tuple val(meta), path(*__evals_e3.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__evals_e3.nii.gz	file	Third eigenvalue.	True	*__evals_e3.{nii,nii.gz}

fa

Format : tuple val(meta), path(*__fa.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__fa.nii.gz	file	Fractional anisotropy.	True	*__fa.{nii,nii.gz}

ga

Format : tuple val(meta), path(*__ga.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__ga.nii.gz	file	Geodesic anisotropy.	True	*__ga.{nii,nii.gz}

rgb

Format : tuple val(meta), path(*__rgb.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__rgb.nii.gz	file	Colored fractional anisotropy.	True	*__rgb.{nii,nii.gz}

md

Format : tuple val(meta), path(*__md.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__md.nii.gz	file	Mean diffusivity.	True	*__md.{nii,nii.gz}

mode

Format : tuple val(meta), path(*__mode.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__mode.nii.gz	file	Mode of tensors.	True	*__mode.{nii,nii.gz}

norm

Format : tuple val(meta), path(*__norm.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__norm.nii.gz	file	Norm of tensors.	True	*__norm.{nii,nii.gz}

rd

Format : tuple val(meta), path(*__rd.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__rd.nii.gz	file	Radial diffusivity.	True	*__rd.{nii,nii.gz}

tensor

Format : tuple val(meta), path(*__tensor.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__tensor.nii.gz	file	Tensor coefficients.	True	*__tensor.{nii,nii.gz}

nonphysical

Format : tuple val(meta), path(*__nonphysical.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__nonphysical.nii.gz	file	Map of voxels with physically implausible signals where the mean of b=0 images is below one or more diffusion-weighted images.	True	*__nonphysical.{nii,nii.gz}

pulsation_std_dwi

Format : tuple val(meta), path(*__pulsation_std_dwi.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__pulsation_std_dwi.nii.gz	file	Standard deviation map across all diffusion-weighted images. Shows pulsation and misalignment artifacts.	True	*__pulsation_std_dwi.{nii,nii.gz}

pulsation_std_b0

Format : tuple val(meta), path(*__pulsation_std_b0.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__pulsation_std_b0.nii.gz	file	Standard deviation map across b=0 images if more than one is available. Shows pulsation and misalignment artifacts.	True	*__pulsation_std_b0.{nii,nii.gz}

residual

Format : tuple val(meta), path(*__residual.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual.nii.gz	file	Residual of the tensor fit.	True	*__residual.{nii,nii.gz}

residual_iqr_residuals

Format : tuple val(meta), path(*__residual_iqr_residuals.npy)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_iqr_residuals.npy	file	Interquartile range of the residual of the tensor fit.	True	*__residual_iqr_residuals.npy

residual_mean_residuals

Format : tuple val(meta), path(*__residual_mean_residuals.npy)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_mean_residuals.npy	file	Average of the residual of the tensor fit.	True	*__residual_mean_residuals.npy

residual_q1_residuals

Format : tuple val(meta), path(*__residual_q1_residuals.npy)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_q1_residuals.npy	file	First quartile of the residual of the tensor fit.	True	*__residual_q1_residuals.npy

residual_q3_residuals

Format : tuple val(meta), path(*__residual_q3_residuals.npy)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_q3_residuals.npy	file	Third quartile of the residual of the tensor fit.	True	*__residual_q3_residuals.npy

residual_residuals_stats

Format : tuple val(meta), path(*__residual_residuals_stats.png)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_residuals_stats.png	file	Complete statistics of the residual of the tensor fit.	True	*__residual_residuals_stats.png

residual_std_residuals

Format : tuple val(meta), path(*__residual_std_residuals.npy)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__residual_std_residuals.npy	file	Standard deviation of the residual of the tensor fit.	True	*__residual_std_residuals.npy

mqc

Format : tuple val(meta), path(*__dti_mqc.png)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__dti_mqc.png	file	.png file containing screenshots of some DTI metrics. Made for use in MultiQC report.	True

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

---

Arguments (see process.ext)

	Type	Description	Default	Choices
dwi_shell_tolerance	integer	Tolerance for the shell detection algorithm.	20
max_dti_shell_value	integer	Maximum value for the DTI shell.	1500
b0_thr_extract_b0	integer	Threshold for the b0 extraction.	0
b0_threshold	integer	Threshold for the b0 mask.	0
dti_shells	string	List of b-values to use for the DTI computation.	0 1000
b0mask	boolean	Use the b0 mask to mask the input image.	True
ad	boolean	Compute the axial diffusivity.	True
evecs	boolean	Compute the eigenvectors of the tensor.	True
evals	boolean	Compute the eigenvalues of the tensor.	True
fa	boolean	Compute the fractional anisotropy.	True
ga	boolean	Compute the geodesic anisotropy.	True
rgb	boolean	Compute the colored fractional anisotropy.	True
md	boolean	Compute the mean diffusivity.	True
mode	boolean	Compute the mode.	True
norm	boolean	Compute the tensor norm.	True
rd	boolean	Compute the radial diffusivity.	True
tensor	boolean	Compute the tensor coefficients.	True
nonphysical	boolean	Compute the nonphysical voxels.	True
pulsation	boolean	Compute the pulsation.	True
residual	boolean	Compute the residual.	True

---

Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

---

Authors

• @scilus

---

Last updated : 2025-10-30