qsiprep.workflows.anatomical package

qsiprep.workflows.anatomical.init_anat_preproc_wf(num_anat_images, num_additional_t2ws, has_rois, anatomical_template, name='anat_preproc_wf')[source]

This workflow controls the anatomical preprocessing stages of qsiprep.

This includes:

  • Creation of a structural template (AC-PC aligned)

  • Skull-stripping and bias correction

  • Tissue segmentation

  • Normalization

(Source code)

Parameters:

  • num_anat_images (int) – Number of anatomical images available in the chosen modality

  • num_additional_t2ws (int) – If anat modality is T1w and there are available T2ws that can be used by DRBUDDI, how many are there?

  • has_rois (bool) – Are there lesion ROI files?

Inputs:

  • t1w – List of T1-weighted structural images

  • t2w – List of T2-weighted structural images

  • flair – List of FLAIR images

  • roi – A mask to exclude regions during standardization (as list)

  • subjects_dir – FreeSurfer SUBJECTS_DIR

Outputs:

  • t1_preproc – Bias-corrected structural template, defining T1w space

  • t1_brain – Skull-stripped t1_preproc

  • t1_mask – Mask of the skull-stripped template image

  • t1_seg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

  • t1_tpms – List of tissue probability maps in T1w space

  • t2_preproc – List of preprocessed t2w files

  • t1_2_mni – T1w template, normalized to MNI space

  • t1_2_mni_forward_transform – ANTs-compatible affine-and-warp transform file

  • t1_2_mni_reverse_transform – ANTs-compatible affine-and-warp transform file (inverse)

  • t1_resampling_grid – Image of the preprocessed t1 to be used as the reference output for dwis

qsiprep.workflows.anatomical.init_synthseg_wf() → LiterateWorkflow[source]
qsiprep.workflows.anatomical.init_synthstrip_wf(do_padding=False, unfatsat=False, name='synthstrip_wf') → LiterateWorkflow[source]

Submodules