.. AUTO-GENERATED FILE -- DO NOT EDIT!

workflows.smri.freesurfer.recon
===============================


.. module:: nipype.workflows.smri.freesurfer.recon


.. _nipype.workflows.smri.freesurfer.recon.create_skullstripped_recon_flow:

:func:`create_skullstripped_recon_flow`
---------------------------------------

`Link to code <file:///build/nipype-4ReYCB/nipype-0.11.0/nipype/workflows/smri/freesurfer/recon.py#L5>`__



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()  # doctest: +SKIP


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
~~~~~

.. graphviz::

	digraph skullstripped_recon_all{

	  label="skullstripped_recon_all";

	  skullstripped_recon_all_inputspec[label="inputspec (utility)"];

	  skullstripped_recon_all_autorecon1[label="autorecon1 (freesurfer)"];

	  skullstripped_recon_all_link_masks[label="link_masks (utility)"];

	  skullstripped_recon_all_autorecon_resume[label="autorecon_resume (freesurfer)"];

	  skullstripped_recon_all_outputspec[label="outputspec (utility)"];

	  skullstripped_recon_all_inputspec -> skullstripped_recon_all_autorecon1;

	  skullstripped_recon_all_inputspec -> skullstripped_recon_all_autorecon1;

	  skullstripped_recon_all_inputspec -> skullstripped_recon_all_autorecon1;

	  skullstripped_recon_all_autorecon1 -> skullstripped_recon_all_link_masks;

	  skullstripped_recon_all_autorecon1 -> skullstripped_recon_all_link_masks;

	  skullstripped_recon_all_link_masks -> skullstripped_recon_all_autorecon_resume;

	  skullstripped_recon_all_link_masks -> skullstripped_recon_all_autorecon_resume;

	  skullstripped_recon_all_autorecon_resume -> skullstripped_recon_all_outputspec;

	  skullstripped_recon_all_autorecon_resume -> skullstripped_recon_all_outputspec;

	}

