List of Output Files

The number of output files generated by PyDesigner may seem very daunting at first. However, once a certain level of familiarity is achieved, it becomes very easy.

There are generally three types of outputs:

1. Preocessing files: files used in preprocessing; stored in root output directory 2. Metric files: DTI/DKI parameters maps, stored in /metrics folder 3. QC Metrics: files that enable data quality control; stored in /metrics_qc

The list of ever possible output file is given in the table below.

Filename

Description

Root Directory

B0.nii

mean b0 image extracted from processed DWI (exists only if:code:–mask is used)

brain_mask.nii

brain mask extracted from B0.nii (exists only if --mask is used)

dwi_preprocessed.nii

fully preprocessed DWI NifTi file

dwi_preprocessed.bval

fully preprocessed DWI’s BVAL file in FSL format

dwi_preprocessed.bvec

fully preprocessed DWI’s BVEC file in FSL format

dwi_preprocessed.json

fully preprocessed DWI’s BIDS sidecar

dwi_raw.nii

raw DWI NifTi file before preprocessing

dwi_raw.bval

raw DWI’s BVAL file in FSL format

dwi_raw.bvec

raw DWI’s BVEC file in FSL format

dwi_raw.json

raw DWI’s BIDS sidecar

noisemap.nii

noisemap NifTi file produced from denoising (exists only if --denoise is used)

working.mif

MRtrix3 file formatted DWI that is being preprocessed

log_command.json

history of preprocessing steps and commands run of DWI

QC Metrics root_dir/metrics_qc

head_motion.png

estimated head motion plotted from displacement field computed by EPI and eddy current correction (exists if --undistort is used)

outliers

plot of percentage outliers detected by IRLLS outlier detection

SNR.png

snr plots of dwi_raw.nii and dwi_preprocessed.nii

/fitting/outliers_akc.nii

outliers detected by brute forced kurtosis tensor outlier rejection algorithm (3d nifti)

/fitting/outliers_irlls.nii

outliers voxels detected by irlls outlier detection (4d nifti)

/eddy

all outputs of the eddy correction (exists if --undistort is used)

DTI/DKI Metrics root_dir/metrics

ad.nii

axial diffusivity map (3d nifti)

rd.nii

radial diffusivity map (3d nifti)

md.nii

mean diffusivity map (3d nifti)

fa.nii

fractional anisotropy map (3d nifti)

fe.nii

first eigenvalues; represents the principal direction of water (4d nifti)

trace.nii

sum of diagnols of in diffusion tensor (3d nifti); the mean diffusivity (MD) is three times the trace [MD 3 * trace ]

ak.nii

axial kurtosis map (3 nifti)

rk.nii

radial kurtosis map (3d nifti)

mk.nii

mean kurtosis map (3d nifti)

kfa.nii

kurtosis fractional anisotropy map (3d nifti)

mkt.nii

mean kurtosis tensor (3d nifti); alternative calculation for mean kurtosis

DT.nii

diffusion tensor (4d nifti; 6 three-dimensional volumes)

KT.nii

kurtosis tensor (4d nifti; 15 three dimensional volumes)

WMTI Metrics root_dir/metrics

wmti_awf.nii

axonal water fraction (3d nifti)

wmti_eas_ad

extra-axonal axial diffusivity (3d nifti)

wmti_eas_rd

extra-axonal radial diffusivity (3d nifti)

wmti_eas_md

extra-axonal mean diffusivity (3d nifti)

wmti_eas_tort

extra-axonal tortuosity (3d nifti)

wmti_ias_ad

intra-axonal axial diffusivity (3d nifti)

wmti_ias_rd

intra-axonal radial diffusivity (3d nifti)

wmti_ias_da

intra-axonal intrinsic diffusivity (3d nifti)

wmti_ias_tort

intra-axonal tortuosity (3d nifti)

All other files in folder /intermediate_nifti are used by PyDesigner for preprocessing flow control, especially to allow --resume or --force flags to work as intended.