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_files (a 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_dir (a 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:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

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

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

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

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

  • max_fwhm_mm (a 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_scale (a boolean) – Disable SPM-like per-volume intensity scaling. Maps to a command-line argument: --no-intensity-scale.

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

  • register_to_first (a 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_resampled (a boolean) – Write resampled copies of the inputs in reference space. Maps to a command-line argument: --save-resampled.

  • save_template (a boolean) – Save the reference volume used as the alignment target. Maps to a command-line argument: --save-template.

  • set_zooms_from_sform (a boolean) – Copy pixdim/zooms from the sform when updating headers. Maps to a command-line argument: --set-zooms-from-sform.

  • update_headers (a boolean) – Only update the NIfTI headers with the estimated affines; do not write resampled volumes. Maps to a command-line argument: --update-headers.

  • use_skullstrip (a boolean) – Estimate transforms on skull-stripped copies of the inputs. Maps to a command-line argument: --use-skullstrip.

  • verbose (a boolean) – Print optimizer diagnostics. Maps to a command-line argument: --verbose.

Outputs:

out_dir (a pathlike object or string representing a directory) – Top-level output directory.