workflows.smri.freesurfer.recon¶
create_skullstripped_recon_flow()
¶
Performs recon-all on voulmes that are already skull stripped. FreeSurfer failes to perform skullstrippig on some volumes (especially MP2RAGE). This can be avoided by doing skullstripping before runnig recon-all (using for example SPECTRE algorithm)
Example¶
>>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
>>> recon_flow = create_skullstripped_recon_flow()
>>> recon_flow.inputs.inputspec.subject_id = 'subj1'
>>> recon_flow.inputs.inputspec.T1_files = 'T1.nii.gz'
>>> recon_flow.run()
- Inputs::
- inputspec.T1_files : skullstripped T1_files (mandatory) inputspec.subject_id : freesurfer subject id (optional) inputspec.subjects_dir : freesurfer subjects directory (optional)
Outputs:
outputspec.subject_id : freesurfer subject id
outputspec.subjects_dir : freesurfer subjects directory
Graph¶