qsirecon.workflows.recon.anatomical module

qsirecon.workflows.recon.anatomical.check_hsv_inputs(subj_fs_path)[source]

Determine if a FreeSurfer directory has the required files for HSV.

qsirecon.workflows.recon.anatomical.init_dwi_recon_anatomical_workflow(atlas_configs, has_qsiprep_5tt_hsvs, needs_t1w_transform, has_freesurfer_5tt_hsvs, has_qsiprep_t1w, has_qsiprep_t1w_transforms, has_freesurfer, extras_to_make, name, template_output_space, prefer_dwi_mask=False)[source]

Ensure that anatomical data is available for the reconstruction workflows.

This workflow calculates images/transforms that require a DWI spatial reference. Specifically, three additional features are added:

  • "dwi_mask": a brain mask in the voxel space of the DWI

  • "atlas_configs": A dictionary used by connectivity workflows to get brain parcellations.

  • "odf_rois": An image with some interesting ROIs for plotting ODFs

Parameters:

  • has_qsiprep_5tt_hsvs (bool)

  • has_freesurfer_5tt_hsvs (bool)

  • has_qsiprep_t1w (bool)

  • has_qsiprep_t1w_transforms (bool)

Returns:

  • workflow (nipype Workflow) – The workflow that calculates the necessary anatomical data

  • status (dict) – A dictionary with the status of the anatomical data, with the following keys:

    • has_qsiprep_5tt_hsvs

    • has_freesurfer_5tt_hsvs

    • has_qsiprep_t1w

    • has_qsiprep_t1w_transforms

    Each value is a boolean indicating whether the data is available.

qsirecon.workflows.recon.anatomical.init_highres_recon_anatomical_wf(subject_id, session_id, extras_to_make, status, name='recon_anatomical_wf')[source]

Gather any high-res anatomical data (images, transforms, segmentations) to use in recon workflows.

This workflow searches through input data to see what anatomical data is available. The anatomical data may be in a freesurfer directory.

qsirecon.workflows.recon.anatomical.init_output_grid_wf() → LiterateWorkflow[source]

Generate a non-oblique, uniform voxel-size grid around a brain.

qsirecon.workflows.recon.anatomical.init_register_fs_to_qsiprep_wf(use_qsiprep_reference_mask=False, name='register_fs_to_qsiprep_wf')[source]

Registers a T1w images from freesurfer to another image and transforms