Command Line¶
The kwneuro command provides file-based entry points for common one-step
workflows. It is meant for quick checks, shell scripts, and interoperability
with existing file workflows. For custom pipelines, reusable Python code, and
fine-grained resource control, use the Python API directly.
kwneuro¶
Run common kwneuro file-based workflows.
Usage
kwneuro [OPTIONS] COMMAND [ARGS]...
dwi¶
DWI commands.
Usage
kwneuro dwi [OPTIONS] COMMAND [ARGS]...
denoise¶
Denoise a DWI and write NIfTI/FSL outputs.
Usage
kwneuro dwi denoise [OPTIONS]
Options
- --dwi <dwi_path>¶
Required
- --bval <bval>¶
- --bvec <bvec>¶
- --out-dwi <out_dwi>¶
Required
dti¶
Fit DTI and optionally write FA/MD maps.
Usage
kwneuro dwi dti [OPTIONS]
Options
- --dwi <dwi_path>¶
Required
- --bval <bval>¶
- --bvec <bvec>¶
- --mask <mask_path>¶
- --out-dti <out_dti>¶
Required
- --out-fa <out_fa>¶
- --out-md <out_md>¶
mean-b0¶
Compute the mean b=0 image from a DWI.
Usage
kwneuro dwi mean-b0 [OPTIONS]
Options
- --dwi <dwi_path>¶
Required
- --bval <bval>¶
- --bvec <bvec>¶
- --out <out_path>¶
Required
mask¶
Brain mask commands.
Usage
kwneuro mask [OPTIONS] COMMAND [ARGS]...
dwi-batch¶
Batch brain extraction for DWI files under an input directory.
Usage
kwneuro mask dwi-batch [OPTIONS]
Options
- --inputs <inputs>¶
Required
- --outputs <outputs>¶
Required
- --sequential¶
Disable HD-BET multiprocessing for embedded Python environments.
structural-batch¶
Batch brain extraction for structural NIfTI files under an input directory.
Usage
kwneuro mask structural-batch [OPTIONS]
Options
- --inputs <inputs>¶
Required
- --outputs <outputs>¶
Required
- --sequential¶
Disable HD-BET multiprocessing for embedded Python environments.
registration¶
Registration and transform commands.
Usage
kwneuro registration [OPTIONS] COMMAND [ARGS]...
apply¶
Apply a saved transform to a moving volume.
Usage
kwneuro registration apply [OPTIONS]
Options
- --transform <transform_dir>¶
Required
- --fixed <fixed_path>¶
Required
- --moving <moving_path>¶
Required
- --out <out_path>¶
Required
- --invert¶
- --interpolation <interpolation>¶
- Default:
'linear'
dwi-to-structural¶
Register a DWI mean b0 image to a structural image.
Usage
kwneuro registration dwi-to-structural [OPTIONS]
Options
- --dwi <dwi_path>¶
Required
- --bval <bval>¶
- --bvec <bvec>¶
- --structural <structural_path>¶
Required
- --out-transform <out_transform>¶
Required
- --transform <type_of_transform>¶
- Default:
'Rigid'
- --dwi-mask <dwi_mask_path>¶
- --structural-mask <structural_mask_path>¶
volumes¶
Register a scalar moving volume to a fixed reference volume.
Usage
kwneuro registration volumes [OPTIONS]
Options
- --fixed <fixed_path>¶
Required
- --moving <moving_path>¶
Required
- --out <out_path>¶
Required
- --out-transform <out_transform>¶
Required
- --transform <type_of_transform>¶
- Default:
'SyN'
- --mask <mask_path>¶
- --moving-mask <moving_mask_path>¶
structural¶
Structural MRI commands.
Usage
kwneuro structural [OPTIONS] COMMAND [ARGS]...
bias-correct¶
Apply N4 bias-field correction to a structural image.
Usage
kwneuro structural bias-correct [OPTIONS]
Options
- --image <image_path>¶
Required
- --out <out_path>¶
Required
extract-brain¶
Extract a brain mask from a structural image.
Usage
kwneuro structural extract-brain [OPTIONS]
Options
- --image <image_path>¶
Required
- --out-mask <out_mask>¶
Required
parcellate¶
Parcellate a structural image.
Usage
kwneuro structural parcellate [OPTIONS]
Options
- --image <image_path>¶
Required
- --out <out_path>¶
Required
- --method <method>¶
- Default:
'dkt'- Options:
dkt
segment-tissues¶
Segment structural image tissues into labeled classes.
Usage
kwneuro structural segment-tissues [OPTIONS]
Options
- --image <image_path>¶
Required
- --out <out_path>¶
Required
- --mask <mask_path>¶
- --method <method>¶
- Default:
'atropos'- Options:
atropos | deep_atropos