nipype.interfaces.t1prep.longitudinal module

Nipype interfaces for T1Prep longitudinal processing.

T1PrepRealignLongitudinal

Rigid realignment of a series of 3D NIfTI volumes acquired from the same subject (longitudinal time-points), mirroring SPM’s realign module. Wraps python -m t1prep.realign_longitudinal.

class nipype.interfaces.t1prep.longitudinal.T1PrepRealignLongitudinal(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: T1PrepCommand

Wrapped executable: python.

Nipype interface for the T1Prep longitudinal realignment module.

Estimates per-timepoint rigid (6-DoF) transforms and optionally refines them against a mean template, then writes resampled volumes and/or updates NIfTI headers in place. Mirrors SPM’s realign module.

Invoked as python -m t1prep.realign_longitudinal.

Examples

>>> ra = T1PrepRealignLongitudinal()
>>> ra.inputs.in_files = ['sub-01_ses-01_T1w.nii.gz', 'sub-01_ses-02_T1w.nii.gz']
>>> ra.inputs.out_dir = 'derivatives/realign'
>>> ra.inputs.save_resampled = True
>>> ra.cmdline
'python -m t1prep.realign_longitudinal --inputs sub-01_ses-01_T1w.nii.gz sub-01_ses-02_T1w.nii.gz --out-dir derivatives/realign --save-resampled'

References

https://github.com/ChristianGaser/T1Prep

Mandatory Inputs

in_filesa list of items which are a pathlike object or string representing an existing file

Input NIfTI images (one per longitudinal time-point). Maps to a command-line argument: --inputs %s.

out_dira pathlike object or string representing a directory

Output directory for realigned volumes and transforms. Maps to a command-line argument: --out-dir %s.

Optional Inputs

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

devicea string

Compute device (currently reserved; default ‘cpu’). Maps to a command-line argument: --device %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

force_template_zoomsa boolean

Force the reference (template) zooms on all outputs. Maps to a command-line argument: --force-template-zooms.

grad_quantilea float

Quantile threshold for the gradient sampler (only used when sample_strategy=’gradient’; default 0.80). Maps to a command-line argument: --grad-quantile %g.

inverse_consistenta boolean

Re-center rigid transforms around their SE(3) barycenter. Maps to a command-line argument: --inverse-consistent.

iterationsan integer

Number of multi-scale alignment passes (default 3). Maps to a command-line argument: --iterations %d.

max_fwhm_mma float

Maximum smoothing FWHM in mm for the multi-scale pyramid (default 6.0). Maps to a command-line argument: --max-fwhm-mm %g.

no_intensity_scalea boolean

Disable SPM-like per-volume intensity scaling. Maps to a command-line argument: --no-intensity-scale.

out_subfoldersa list of items which are a string

Per-input output subfolder names (must match the number of inputs). Maps to a command-line argument: --out-subfolders %s.

output_naming‘bids’ or ‘legacy’

Output naming convention: ‘bids’ (default) or ‘legacy’. Maps to a command-line argument: --output-naming %s.

overlap_penalty_weighta float

Weight of the overlap penalty term (default 0.0). Maps to a command-line argument: --overlap-penalty-weight %g.

register_to_firsta boolean

Register all volumes to the first input (skip mean-template refinement). Maps to a command-line argument: --register-to-first.

sample_strategy‘grid’ or ‘gradient’

Sample-point selection: ‘grid’ (default) or ‘gradient’. Maps to a command-line argument: --sample-strategy %s.

save_resampleda boolean

Write resampled copies of the inputs in reference space. Maps to a command-line argument: --save-resampled.

save_templatea boolean

Save the reference volume used as the alignment target. Maps to a command-line argument: --save-template.

set_zooms_from_sforma boolean

Copy pixdim/zooms from the sform when updating headers. Maps to a command-line argument: --set-zooms-from-sform.

update_headersa boolean

Only update the NIfTI headers with the estimated affines; do not write resampled volumes. Maps to a command-line argument: --update-headers.

use_skullstripa boolean

Estimate transforms on skull-stripped copies of the inputs. Maps to a command-line argument: --use-skullstrip.

verbosea boolean

Print optimizer diagnostics. Maps to a command-line argument: --verbose.

Outputs

out_dira pathlike object or string representing a directory

Top-level output directory.