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# workflows.smri.freesurfer.recon

## `create_skullstripped_recon_flow()`

Link to code

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