graphpype.pipelines.create_pipeline_nii_to_conmat_simple

graphpype.pipelines.create_pipeline_nii_to_conmat_simple(main_path, pipeline_name='nii_to_conmat', conf_interval_prob=0.05, background_val=-1.0, plot=True)[source]

Pipeline from nifti 4D (after preprocessing) to connectivity matrices, no segmentation in tissues given, but coords for wm and csf are available and regressed. coords / labels o indexed mask are also available

Inputs (inputnode):

  • nii_4D_file
  • ROI_mask_file
Optional inputs (inputnode) :
  • rp_file
  • ROI_coords_file
  • ROI_MNI_coords_file
  • ROI_labels_file

Comments:

Typically used after nipype preprocessing pipeline and before conmat_to_graph pipeline