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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

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;

}