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

nipype.workflows.freesurfer.utils
=================================


:class:`create_get_stats_flow()`
--------------------------------


Retrieves stats from labels

Parameters
~~~~~~~~~~

name : string
    name of workflow
withreg : boolean
    indicates whether to register source to label

Example
~~~~~~~


Inputs::

       inputspec.source_file : reference image for mask generation
       inputspec.label_file : label file from which to get ROIs

       (optionally with registration)
       inputspec.reg_file : bbreg file (assumes reg from source to label
       inputspec.inverse : boolean whether to invert the registration
       inputspec.subjects_dir : freesurfer subjects directory

Outputs::

       outputspec.stats_file : stats file



Graph
~~~~~
.. graphviz::

	digraph getstats{

	  label="getstats";

	  getstats_inputspec[label="inputspec.IdentityInterface.utility"];

	  getstats_segstats[label="segstats.SegStats.freesurfer"];

	  getstats_outputspec[label="outputspec.IdentityInterface.utility"];

	  getstats_inputspec -> getstats_segstats;

	  getstats_inputspec -> getstats_segstats;

	  getstats_segstats -> getstats_outputspec;

	}

:class:`create_getmask_flow()`
------------------------------


Registers a source file to freesurfer space and create a brain mask in
source space

Requires fsl tools for initializing registration

Parameters
~~~~~~~~~~

name : string
    name of workflow
dilate_mask : boolean
    indicates whether to dilate mask or not

Example
~~~~~~~

>>> getmask = create_getmask_flow()
>>> getmask.inputs.inputspec.source_file = 'mean.nii'
>>> getmask.inputs.inputspec.subject_id = 's1'
>>> getmask.inputs.inputspec.subjects_dir = '.'
>>> getmask.inputs.inputspec.contrast_type = 't2'


Inputs::

       inputspec.source_file : reference image for mask generation
       inputspec.subject_id : freesurfer subject id
       inputspec.subjects_dir : freesurfer subjects directory
       inputspec.contrast_type : MR contrast of reference image

Outputs::

       outputspec.mask_file : binary mask file in reference image space
       outputspec.reg_file : registration file that maps reference image to
                             freesurfer space
       outputspec.reg_cost : cost of registration (useful for detecting misalignment)



Graph
~~~~~
.. graphviz::

	digraph getmask{

	  label="getmask";

	  getmask_inputspec[label="inputspec.IdentityInterface.utility"];

	  getmask_fssource[label="fssource.FreeSurferSource.io"];

	  getmask_register[label="register.BBRegister.freesurfer"];

	  getmask_threshold[label="threshold.Binarize.freesurfer"];

	  getmask_transform[label="transform.ApplyVolTransform.freesurfer"];

	  getmask_dilate[label="dilate.DilateImage.fsl"];

	  getmask_threshold2[label="threshold2.Binarize.freesurfer"];

	  getmask_outputspec[label="outputspec.IdentityInterface.utility"];

	  getmask_inputspec -> getmask_fssource;

	  getmask_inputspec -> getmask_fssource;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_transform;

	  getmask_inputspec -> getmask_transform;

	  getmask_fssource -> getmask_threshold;

	  getmask_register -> getmask_transform;

	  getmask_register -> getmask_outputspec;

	  getmask_register -> getmask_outputspec;

	  getmask_threshold -> getmask_transform;

	  getmask_transform -> getmask_dilate;

	  getmask_dilate -> getmask_threshold2;

	  getmask_threshold2 -> getmask_outputspec;

	}
