/Users/bsipes/opt/anaconda3/envs/tracts/lib/python3.9/site-packages/bids/config.py:39: FutureWarning: Setting 'extension_initial_dot' will be removed in pybids 0.16.
  warnings.warn("Setting 'extension_initial_dot' will be removed in pybids 0.16.",
/Users/bsipes/opt/anaconda3/envs/tracts/lib/python3.9/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "

class PreProcNodes[source]

PreProcNodes(bids_dir, bids_path_template, bids_ext, rpe_design, mrtrix_nthreads, img_resol, sub_list, ses_list, exclude_list=[()])

Initiate DWI preprocessing pipeline nodes. This doesn't connect the nodes into a pipeline.

Inputs:

- bids_dir (str) -
- bids_path_template (dict) - template for file naming conventions
- bids_ext (str) -
- rpe_design (str) - This is necessary to initiate nodes for single DWI volume, or additional nodes for reverse volume.
- mrtrix_nthreads (int)
- img_resol (str)
- sub_list (List)
- ses_list (List)
- exclude_list (tuple)

class ACPCNodes[source]

ACPCNodes(MNI_template)

T1 anatomy image related nodes. Mainly ACPC alignment of T1 and DWI and extraction of white matter mask. Inputs:

- MNI_template: path to MNI template provided by FSL. By default uses the environment variable FSLDIR to locate the reference templates for ACPC alignment.

Post-processing Nodes

Nodes for fetching streamlines, MRI, atlases and combine into connectomes.

class PostProcNodes[source]

PostProcNodes(BIDS_dir, subj_template, sub_list, ses_list, skip_tuples)

Inputs: BIDS_dir (str): Path to BIDS directory subj_template (dict): template directory for tck, dwi, T1, mask files sub_list (list): subjects IDs list generated from BIDS layout ses_list (list): sessions IDs listgenerated from BIDS layout skip_tuples (tuple): [('subject', 'session')] string pair to skip