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 |
|
|
mean b0 image extracted from processed DWI (exists only if:code:–mask is used) |
|
brain mask extracted from B0.nii (exists only if
|
|
fully preprocessed DWI NifTi file |
|
fully preprocessed DWI’s BVAL file in FSL format |
|
fully preprocessed DWI’s BVEC file in FSL format |
|
fully preprocessed DWI’s BIDS sidecar |
|
raw DWI NifTi file before preprocessing |
|
raw DWI’s BVAL file in FSL format |
|
raw DWI’s BVEC file in FSL format |
|
raw DWI’s BIDS sidecar |
|
noisemap NifTi file produced from denoising (exists
only if |
|
MRtrix3 file formatted DWI that is being preprocessed |
|
history of preprocessing steps and commands run of DWI |
QC Metrics |
|
|
estimated head motion plotted from displacement field
computed by EPI and eddy current correction (exists if
|
|
plot of percentage outliers detected by IRLLS outlier detection |
|
snr plots of dwi_raw.nii and dwi_preprocessed.nii |
|
outliers detected by brute forced kurtosis tensor outlier rejection algorithm (3d nifti) |
|
outliers voxels detected by irlls outlier detection (4d nifti) |
|
all outputs of the eddy correction (exists if
|
DTI/DKI Metrics |
|
|
axial diffusivity map (3d nifti) |
|
radial diffusivity map (3d nifti) |
|
mean diffusivity map (3d nifti) |
|
fractional anisotropy map (3d nifti) |
|
first eigenvalues; represents the principal direction of water (4d nifti) |
|
sum of diagnols of in diffusion tensor (3d nifti); the mean diffusivity (MD) is three times the trace [MD 3 * trace ] |
|
axial kurtosis map (3 nifti) |
|
radial kurtosis map (3d nifti) |
|
mean kurtosis map (3d nifti) |
|
kurtosis fractional anisotropy map (3d nifti) |
|
mean kurtosis tensor (3d nifti); alternative calculation for mean kurtosis |
|
diffusion tensor (4d nifti; 6 three-dimensional volumes) |
|
kurtosis tensor (4d nifti; 15 three dimensional volumes) |
WMTI Metrics |
|
|
axonal water fraction (3d nifti) |
|
extra-axonal axial diffusivity (3d nifti) |
|
extra-axonal radial diffusivity (3d nifti) |
|
extra-axonal mean diffusivity (3d nifti) |
|
extra-axonal tortuosity (3d nifti) |
|
intra-axonal axial diffusivity (3d nifti) |
|
intra-axonal radial diffusivity (3d nifti) |
|
intra-axonal intrinsic diffusivity (3d nifti) |
|
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.