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