Note
This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.
brainprep.workflow.brainprep_longitudinal_sbm¶
- brainprep.workflow.brainprep_longitudinal_sbm(t1_files, output_dir, keep_intermediate=False, **kwargs)[source]¶
Longitudinal SBM preprocessing.
Applies the longitudinal brain parcellation pre-processing described in [1]. This includes:
the creation of a template for this subject.
the parcellation refinements from the new generated template.
- Parameters:
- t1_fileslist[File]
Path to the t1 images.
- output_dirDirectory
FreeSurfer working directory containing all the subjects.
- keep_intermediatebool
If True, retains intermediate results (i.e., the workspace); useful for debugging. Default False.
- **kwargsdict
- entities: list[dict]
Dictionaries of parsed BIDS entities.
- Returns:
- Bunch
A dictionary-like object containing:
subject_dirs: list[Directory] - the FreeSurfer subject directories.
- Raises:
- ValueError
If the input T1w files are not BIDS-compliant.
Notes
This workflow assumes the T1w images are organized in BIDS.
References
Examples
>>> from brainprep.config import Config >>> from brainprep.reporting import RSTReport >>> from brainprep.workflow import brainprep_longitudinal_sbm >>> >>> with Config(dryrun=True, verbose=False): ... report = RSTReport() ... outputs = brainprep_longitudinal_sbm( ... t1_files=[ ... "/tmp/dataset/rawdata/sub-01/ses-01/anat/" ... "sub-01_ses-01_run-01_T1w.nii.gz", ... "/tmp/dataset/rawdata/sub-01/ses-02/anat/" ... "sub-01_ses-02_run-01_T1w.nii.gz", ... ], ... output_dir="/tmp/dataset/derivatives", ... ) >>> outputs Bunch( subject_dirs: [PosixPath('...'), PosixPath('...')] )
