5. List of commands from sammba-MRI¶
Sammba-MRI is an application programming interface (API). Its modules are presented underneath.
List of modules
sammba.io_conversions: From scanner (DICOM files from Bruker) to NIFTIsammba.data_fetchers: To fetch specific datasets and atlassammba.registration: Registration utilitiessammba.segmentation: Segmentation utilitiessammba.graphs: Pipeline graphs- External tools wrapped in python
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DEPRECATED: Function ‘anats_to_template’ has been replaced by function ‘anat_to_template’ and will be removed in future release.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) |
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5.5. sammba.graphs: Pipeline graphs¶
Functions:
create_pipeline_graph(pipeline_name, graph_file) |
Creates pipeline graph for a given piepline. |