Module: reconst/dtimetrics
Script to compute all of the Diffusion Tensor Imaging (DTI) metrics
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| dwi | file | Nifti DWI volume used to extract DTI metrics. | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | *.bval |
| bvec | file | B-vectors in FSL format. | *.bvec |
| b0mask | file | Nifti b0 volume file used to mask the input image. | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| ad | file | Output filename for the axial diffusivity. | *__ad.{nii,nii.gz} |
| evecs | file | Output filename for the eigenvectors of the tensor. | *__evecs.{nii,nii.gz} |
| evecs_v1 | file | Output filename for the first eigenvector. | *__evecs_v1.{nii,nii.gz} |
| evecs_v2 | file | Output filename for the second eigenvector. | *__evecs_v2.{nii,nii.gz} |
| evecs_v3 | file | Output filename for the third eigenvector. | *__evecs_v3.{nii,nii.gz} |
| evals | file | Output filename for the eigenvalues of the tensor. | *__evals.{nii,nii.gz} |
| evals_e1 | file | Output filename for the first eigenvalue. | *__evals_e1.{nii,nii.gz} |
| evals_e2 | file | Output filename for the second eigenvalue. | *__evals_e2.{nii,nii.gz} |
| evals_e3 | file | Output filename for the third eigenvalue. | *__evals_e3.{nii,nii.gz} |
| fa | file | Output filename for the fractional anisotropy. | *__fa.{nii,nii.gz} |
| ga | file | Output filename for the geodesic anisotropy. | *__ga.{nii,nii.gz} |
| rgb | file | Output filename for the colored fractional anisotropy. | *__rgb.{nii,nii.gz} |
| md | file | Output filename for the mean diffusivity. | *__md.{nii,nii.gz} |
| mode | file | Output filename for the mode. | *__mode.{nii,nii.gz} |
| norm | file | Output filename for the tensor norm. | *__norm.{nii,nii.gz} |
| rd | file | Output filename for the radial diffusivity. | *__rd.{nii,nii.gz} |
| tensor | file | Output filename for the tensor coefficients. | *__tensor.{nii,nii.gz} |
| nonphysical | file | Output filename for the voxels with physically implausible signals where the mean of b=0 images is below one or more diffusion-weighted images. | *__nonphysical.{nii,nii.gz} |
| pulsation_std_dwi | file | Standard deviation map across all diffusion-weighted images. Shows pulsation and misalignment artifacts. | *__pulsation_std_dwi.{nii,nii.gz} |
| pulsation_std_b0 | file | Standard deviation map across b=0 images if more than one is available. Shows pulsation and misalignment artifacts. | *__pulsation_std_b0.{nii,nii.gz} |
| residual | file | Output filename for the map of the residual of the tensor fit. | *__residual.{nii,nii.gz} |
| residual_iqr_residuals | file | Output filename for the interquartile range of the residual of the tensor fit. | *__residual_iqr_residuals.npy |
| residual_mean_residuals | file | Output filename for the mean of the residual of the tensor fit. | *__residual_mean_residuals.npy |
| residual_q1_residuals | file | Output filename for the firt quartile of the residual of the tensor fit. | *__residual_q1_residuals.npy |
| residual_q3_residuals | file | Output filename for the third quartile of the residual of the tensor fit. | *__residual_q3_residuals.npy |
| residual_residuals_stats | file | Output filename for the all statistics of the residual of the tensor fit. | *__residual_residuals_stats.png |
| residual_std_residuals | file | Output filename for the standard deviation of the residual of the tensor fit. | *__residual_std_residuals.npy |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git |
Keywords
| nifti |
| DTI |
| tensor |
| scilpy |
Authors
@scilus