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
dti_ad.nii	axial diffusivity map (3d nifti)
dti_rd.nii	radial diffusivity map (3d nifti)
dti_md.nii	mean diffusivity map (3d nifti)
dti_fa.nii	fractional anisotropy map (3d nifti)
dti_fe.nii	first eigenvalues; represents the principal direction of water (4d nifti)
dti_trace.nii	sum of diagnols of in diffusion tensor (3d nifti); the mean diffusivity (MD) is three times the trace [MD 3 * trace ]
dki_ak.nii	axial kurtosis map (3 nifti)
dki_rk.nii	radial kurtosis map (3d nifti)
dki_mk.nii	mean kurtosis map (3d nifti)
dki_kfa.nii	kurtosis fractional anisotropy map (3d nifti)
dki_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)
FBI/FBWM Metrics root_dir/metrics
fbi_zeta.nii	zeta (3d nifti)
fbi_faa.nii	axonal fractional anisotropy (3d nifti)
fbi_fodf.nii	FBI fODFs from spherical harmonic expansion (4d nifti)
fbi_tractography_dsi.fib	FBI fODFs prepared for DSI Studio’s tractography (fib)
fbwm_awf.nii	axonal water fraction (3d nifti)
fbwm_Da.nii	intra-axonal diffusivity (3d nifti)
fbwm_De_ax.nii	axial extra-axonal diffusivity (3d nifti)
fbwm_De_rad.nii	radial extra-axonal diffusivity (3d nifti)
fbwm_De_mean.nii	mean radial extra-axonal diffusivity (3d nifti)
fbwm_fae.nii	extra-axonal fractional anisotropy (3d nifti)
fbwm_minCost.nii	minimum cost computed by cost function (3d nifti)
fbwm_minCost.nii	all costs computed by cost function (4d nifti; 100 three dimensional volumes)
WMTI Metrics root_dir/metrics
wmti_awf.nii	axonal water fraction (3d nifti)
wmti_eas_ad.nii	extra-axonal axial diffusivity (3d nifti)
wmti_eas_rd.nii	extra-axonal radial diffusivity (3d nifti)
wmti_eas_tort.nii	extra-axonal tortuosity (3d nifti)
wmti_ias_da.nii	intra-axonal intrinsic diffusivity (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.