5. List of commands from sammba-MRI

Sammba-MRI is an application programming interface (API). Its modules are presented underneath.

List of modules

5.1. sammba.io_conversions: From scanner (DICOM files from Bruker) to NIFTI

Functions:

dcm_to_nii(dcmdump_path, dicom_filename, …) Converts Bruker Paravision enhanced multiframe DICOM files into NIfTI-1 format.
recursive_dcm_to_nii(dcmdump_path, …) Traverses recursively subdirectories of a given session directory and converts all DICOM files to NIFTI files.

5.2. sammba.data_fetchers: To fetch specific datasets and atlas

Helper functions to download NeuroImaging mouse datasets and atlases

Functions:

fetch_zurich_test_retest([subjects, …]) Download and loads the ETH-Zurich test-retest dataset.
fetch_zurich_anesthesiant([subjects, url, …]) Download and loads the ETH-Zurich anesthesiant dataset.
fetch_atlas_dorr_2008([image_format, …]) Download and load Dorr et al.
fetch_atlas_waxholm_rat_2014([data_dir, …]) Download and load Pape et al.
fetch_masks_dorr_2008([image_format, …]) Downloads DORR 2008 atlas first, then uses its labels to produce tissue masks.
fetch_atlas_lemur_mircen_2019([data_dir, …]) Download and load the MIRCen mouse lemur atlas and average (dated 2017)
fetch_lemur_mircen_2019_t2([subjects, …]) Download and loads the mouse lemur template dataset.

5.3. sammba.registration: Registration utilities

Functions:

anats_to_common(anat_filenames, write_dir, …) Create common template from native anatomical images and achieve their registration to it.
anats_to_template(*args, **kwargs) DEPRECATED: Function ‘anats_to_template’ has been replaced by function ‘anat_to_template’ and will be removed in future release.
fmri_sessions_to_template(*args, **kwargs) DEPRECATED: Function ‘fmri_sessions_to_template’ is deprecated and will be removed in future release.
coregister_fmri_session(*args, **kwargs) DEPRECATED: Function ‘coregister_fmri_session’ is deprecated and will be removed in future release.

Classes:

FMRISession([func, anat, animal_id]) Encapsulation for fMRI data, relative to preprocessing.
TemplateRegistrator(template, brain_volume) Class for registering anatomical and possibly other modality images from one animal to a given head template.
Coregistrator([brain_volume, output_dir, …]) Class for registering anatomical image to perfusion/functional images from one animal in native space.

5.4. sammba.segmentation: Segmentation utilities

Functions:

brain_extraction_report(head_file, brain_volume)
Parameters:

5.5. sammba.graphs: Pipeline graphs

Functions:

create_pipeline_graph(pipeline_name, graph_file) Creates pipeline graph for a given piepline.