niworkflows.interfaces.cifti module#

Handling connectivity: combines FreeSurfer surfaces with subcortical volumes.

class niworkflows.interfaces.cifti.CiftiNameSource(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Construct new filename based on unique label of spaces used to generate a CIFTI file.

Examples

>>> namer = CiftiNameSource()
>>> namer.inputs.variant = 'HCP grayordinates'
>>> res = namer.run()
>>> res.outputs.out_name
'space-fsLR_bold.dtseries'

>>> namer.inputs.density = '32k'
>>> res = namer.run()
>>> res.outputs.out_name
'space-fsLR_den-32k_bold.dtseries'
Mandatory Inputs

variant (a string) – Unique label of spaces used in combination to generate CIFTI file.

Optional Inputs

density (a string) – Density label.

Outputs

out_name (a string) – (partial) filename formatted according to template.

class niworkflows.interfaces.cifti.GenerateCifti(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Generate CIFTI image from BOLD file in target spaces.

Currently supports fsLR, fsaverage5, or fsaverage6 for template surfaces and MNI152NLin6Asym or MNI152NLin2009cAsym as template volumes.

Mandatory Inputs

  • TR (a float) – Repetition time.

  • bold_file (a pathlike object or string representing an existing file) – Input BOLD file.

  • subjects_dir (a pathlike object or string representing a directory) – FreeSurfer SUBJECTS_DIR.

  • surface_bolds (a list of items which are a pathlike object or string representing an existing file) – List of surface BOLD GIFTI files (length 2 with order [L,R]).

Optional Inputs

  • surface_density (‘10k’ or ‘32k’ or ‘41k’ or ‘59k’) – Surface vertices density.

  • surface_target (‘fsLR’ or ‘fsaverage5’ or ‘fsaverage6’) – CIFTI surface target space. (Nipype default value: fsLR)

  • volume_target (‘MNI152NLin6Asym’ or ‘MNI152NLin2009cAsym’) – CIFTI volumetric output space. (Nipype default value: MNI152NLin6Asym)

Outputs

  • density (a string) – Total number of grayordinates.

  • out_file (a pathlike object or string representing an existing file) – Generated CIFTI file.

  • out_metadata (a pathlike object or string representing an existing file) – Variant metadata JSON.

  • variant (a string) – Name of variant space.