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--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 :code:`root_dir/metric | s_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 :code:`root_dir/m | etrics` |
| :code: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 :code:`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 :code:`root_dir/metr | ics` |
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.