smriprep.workflows.anatomical module

Anatomical reference preprocessing workflows.

smriprep.workflows.anatomical.init_anat_preproc_wf(*, bids_root, freesurfer, hires, longitudinal, t1w, t2w, omp_nthreads, output_dir, skull_strip_mode, skull_strip_template, spaces, cifti_output=False, debug=False, existing_derivatives=None, name='anat_preproc_wf', skull_strip_fixed_seed=False)[source]

Stage the anatomical preprocessing steps of sMRIPrep.

This includes:

  • T1w reference: realigning and then averaging T1w images.

  • Brain extraction and INU (bias field) correction.

  • Brain tissue segmentation.

  • Spatial normalization to standard spaces.

  • Surface reconstruction with FreeSurfer.

Workflow Graph
../_images/smriprep-workflows-anatomical-1.png

(Source code, png, svg, pdf)

Parameters:

  • bids_root (str) – Path of the input BIDS dataset root

  • existing_derivatives (dict or None) – Dictionary mapping output specification attribute names and paths to corresponding derivatives.

  • freesurfer (bool) – Enable FreeSurfer surface reconstruction (increases runtime by 6h, at the very least)

  • hires (bool) – Enable sub-millimeter preprocessing in FreeSurfer

  • longitudinal (bool) – Create unbiased structural template, regardless of number of inputs (may increase runtime)

  • t1w (list) – List of T1-weighted structural images.

  • omp_nthreads (int) – Maximum number of threads an individual process may use

  • output_dir (str) – Directory in which to save derivatives

  • skull_strip_template (Reference) – Spatial reference to use in atlas-based brain extraction.

  • spaces (SpatialReferences) – Object containing standard and nonstandard space specifications.

  • debug (bool) – Enable debugging outputs

  • name (str, optional) – Workflow name (default: anat_preproc_wf)

  • skull_strip_mode (str) – Determiner for T1-weighted skull stripping (force ensures skull stripping, skip ignores skull stripping, and auto automatically ignores skull stripping if pre-stripped brains are detected).

  • skull_strip_fixed_seed (bool) – Do not use a random seed for skull-stripping - will ensure run-to-run replicability when used with –omp-nthreads 1 (default: False).

Inputs:

  • t1w – List of T1-weighted structural images

  • t2w – List of T2-weighted structural images

  • roi – A mask to exclude regions during standardization

  • flair – List of FLAIR images

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • subject_id – FreeSurfer subject ID

Outputs:

  • t1w_preproc – The T1w reference map, which is calculated as the average of bias-corrected and preprocessed T1w images, defining the anatomical space.

  • t1w_brain – Skull-stripped t1w_preproc

  • t1w_mask – Brain (binary) mask estimated by brain extraction.

  • t1w_dseg – Brain tissue segmentation of the preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF).

  • t1w_tpms – List of tissue probability maps corresponding to t1w_dseg.

  • std_preproc – T1w reference resampled in one or more standard spaces.

  • std_mask – Mask of skull-stripped template, in MNI space

  • std_dseg – Segmentation, resampled into MNI space

  • std_tpms – List of tissue probability maps in MNI space

  • subjects_dir – FreeSurfer SUBJECTS_DIR

  • anat2std_xfm – Nonlinear spatial transform to resample imaging data given in anatomical space into standard space.

  • std2anat_xfm – Inverse transform of the above.

  • subject_id – FreeSurfer subject ID

  • t1w2fsnative_xfm – LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space

  • fsnative2t1w_xfm – LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w

  • surfaces – GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)

  • morphometrics – GIFTIs of cortical thickness, curvature, and sulcal depth

See also

smriprep.workflows.anatomical.init_anat_template_wf(*, longitudinal: bool, omp_nthreads: int, num_files: int, contrast: str, name: str = 'anat_template_wf')[source]

Generate a canonically-oriented, structural average from all input images.

Workflow Graph
../_images/smriprep-workflows-anatomical-2.png

(Source code, png, svg, pdf)

Parameters:

  • longitudinal (bool) – Create unbiased structural average, regardless of number of inputs (may increase runtime)

  • omp_nthreads (int) – Maximum number of threads an individual process may use

  • num_files (int) – Number of images

  • contrast (str) – Name of contrast, for reporting purposes, e.g., T1w, T2w, PDw

  • name (str, optional) – Workflow name (default: anat_template_wf)

Inputs:

anat_files – List of structural images

Outputs:

  • anat_ref – Structural reference averaging input images

  • anat_valid_list – List of structural images accepted for combination

  • anat_realign_xfm – List of affine transforms to realign input images to final reference

  • out_report – Conformation report