workflows.smri.freesurfer.utils

create_get_stats_flow()

Link to code

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

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; }

create_getmask_flow()

Link to code

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

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_outputspec; getmask_register -> getmask_outputspec; getmask_register -> getmask_transform; getmask_transform -> getmask_threshold2; getmask_threshold2 -> getmask_outputspec; }

create_tessellation_flow()

Link to code

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' 
>>> tessflow.run()

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

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_volconvert; tessellate_fssource -> tessellate_tessellate; 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; }

copy_file()

Link to code

Create a function to copy a file that can be modified by a following node without changing the original file.

copy_files()

Link to code

Create a function to copy a file that can be modified by a following node without changing the original file

get_aparc_aseg()

Link to code

Return the aparc+aseg.mgz file

getdefaultconfig()

Link to code

mkdir_p()

Link to code