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

workflows.smri.freesurfer.utils
===============================


.. module:: nipype.workflows.smri.freesurfer.utils


.. _nipype.workflows.smri.freesurfer.utils.create_get_stats_flow:

:func:`create_get_stats_flow`
-----------------------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/workflows/smri/freesurfer/utils.py#L151>`__



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 (utility)"];

	  getstats_segstats[label="segstats (freesurfer)"];

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

	  getstats_inputspec -> getstats_segstats;

	  getstats_inputspec -> getstats_segstats;

	  getstats_segstats -> getstats_outputspec;

	}


.. _nipype.workflows.smri.freesurfer.utils.create_getmask_flow:

:func:`create_getmask_flow`
---------------------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/workflows/smri/freesurfer/utils.py#L25>`__



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 (utility)"];

	  getmask_fssource[label="fssource (io)"];

	  getmask_threshold[label="threshold (freesurfer)"];

	  getmask_register[label="register (freesurfer)"];

	  getmask_transform[label="transform (freesurfer)"];

	  getmask_threshold2[label="threshold2 (freesurfer)"];

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

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_register;

	  getmask_inputspec -> getmask_fssource;

	  getmask_inputspec -> getmask_fssource;

	  getmask_inputspec -> getmask_transform;

	  getmask_inputspec -> getmask_transform;

	  getmask_fssource -> getmask_threshold;

	  getmask_threshold -> getmask_transform;

	  getmask_register -> getmask_transform;

	  getmask_register -> getmask_outputspec;

	  getmask_register -> getmask_outputspec;

	  getmask_transform -> getmask_threshold2;

	  getmask_threshold2 -> getmask_outputspec;

	}


.. _nipype.workflows.smri.freesurfer.utils.create_tessellation_flow:

:func:`create_tessellation_flow`
--------------------------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/workflows/smri/freesurfer/utils.py#L258>`__



Tessellates the input subject's aseg.mgz volume and returns
the surfaces for each region in stereolithic (.stl) format

Example
~~~~~~~
>>> from nipype.workflows.smri.freesurfer import create_tessellation_flow
>>> tessflow = create_tessellation_flow()
>>> tessflow.inputs.inputspec.subject_id = 'subj1'
>>> tessflow.inputs.inputspec.subjects_dir = '.'
>>> tessflow.inputs.inputspec.lookup_file = 'FreeSurferColorLUT.txt' # doctest: +SKIP
>>> tessflow.run()  # doctest: +SKIP


Inputs::

       inputspec.subject_id : freesurfer subject id
       inputspec.subjects_dir : freesurfer subjects directory
       inputspec.lookup_file : lookup file from freesurfer directory

Outputs::

       outputspec.meshes : output region meshes in (by default) stereolithographic (.stl) format


Graph
~~~~~

.. graphviz::

	digraph tessellate{

	  label="tessellate";

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

	  tessellate_fssource[label="fssource (io)"];

	  tessellate_volconvert[label="volconvert (freesurfer)"];

	  tessellate_region_list_from_volume_node[label="region_list_from_volume_node (utility)"];

	  tessellate_id_list_from_lookup_table_node[label="id_list_from_lookup_table_node (utility)"];

	  tessellate_tessellate[label="tessellate (freesurfer)"];

	  tessellate_surfconvert[label="surfconvert (freesurfer)"];

	  tessellate_smoother[label="smoother (meshfix)"];

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

	  tessellate_inputspec -> tessellate_fssource;

	  tessellate_inputspec -> tessellate_fssource;

	  tessellate_inputspec -> tessellate_id_list_from_lookup_table_node;

	  tessellate_fssource -> tessellate_tessellate;

	  tessellate_fssource -> tessellate_volconvert;

	  tessellate_volconvert -> tessellate_region_list_from_volume_node;

	  tessellate_region_list_from_volume_node -> tessellate_tessellate;

	  tessellate_region_list_from_volume_node -> tessellate_id_list_from_lookup_table_node;

	  tessellate_id_list_from_lookup_table_node -> tessellate_tessellate;

	  tessellate_tessellate -> tessellate_surfconvert;

	  tessellate_surfconvert -> tessellate_smoother;

	  tessellate_smoother -> tessellate_outputspec;

	}


.. _nipype.workflows.smri.freesurfer.utils.get_aparc_aseg:

:func:`get_aparc_aseg`
----------------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/workflows/smri/freesurfer/utils.py#L17>`__



Return the aparc+aseg.mgz file

