User guide: table of contents

• 1. Introduction: Sammba-MRI
  • 1.1. What is sammba-MRI: small-mammal neuroimaging with Python
  • 1.2. First: Install dependencies
    • 1.2.1. Installing Python packages
    • 1.2.2. Installing required neuroimaging software
  • 1.3. Second: Install sammba-MRI
  • 1.4. Third: Run sammba-MRI
• 2. Data conversion
  • 2.1. Data conversion: from DICOM (Bruker-Dicom) to NIfTI-1 format
• 3. Registering several MRI images and creating a template
  • 3.1. Registering several raw MRI images to common space
  • 3.2. Registering several MRI images to template space
• 4. Measuring regional brain volumes
  • 4.1. Step 1 - Registering several MRI images to an existing template
  • 4.2. Step 2 - Align the Atlas on the raw MR images thanks to the deformation evaluated in step 1
  • 4.3. Step 3 - Measure of the volume of each registered ROI of the atlas
• 5. List of commands from sammba-MRI
  • 5.1. sammba.io_conversions: From scanner (DICOM files from Bruker) to NIFTI
    • 5.1.1. sammba.io_conversions.dcm_to_nii
    • 5.1.2. sammba.io_conversions.recursive_dcm_to_nii
  • 5.2. sammba.data_fetchers: To fetch specific datasets and atlas
    • 5.2.1. sammba.data_fetchers.fetch_zurich_test_retest
    • 5.2.2. sammba.data_fetchers.fetch_zurich_anesthesiant
    • 5.2.3. sammba.data_fetchers.fetch_atlas_dorr_2008
    • 5.2.4. sammba.data_fetchers.fetch_atlas_waxholm_rat_2014
    • 5.2.5. sammba.data_fetchers.fetch_masks_dorr_2008
    • 5.2.6. sammba.data_fetchers.fetch_atlas_lemur_mircen_2019
    • 5.2.7. sammba.data_fetchers.fetch_lemur_mircen_2019_t2
  • 5.3. sammba.registration: Registration utilities
    • 5.3.1. sammba.registration.anats_to_common
    • 5.3.2. sammba.registration.anats_to_template
    • 5.3.3. sammba.registration.fmri_sessions_to_template
    • 5.3.4. sammba.registration.coregister_fmri_session
    • 5.3.5. sammba.registration.FMRISession
    • 5.3.6. sammba.registration.TemplateRegistrator
    • 5.3.7. sammba.registration.Coregistrator
  • 5.4. sammba.segmentation: Segmentation utilities
    • 5.4.1. sammba.segmentation.brain_extraction_report
  • 5.5. sammba.graphs: Pipeline graphs
    • 5.5.1. sammba.graphs.create_pipeline_graph
  • 5.6. External tools wrapped in python
    • 5.6.1. segmentation.interfaces
      • 5.6.1.1. HistogramMask
        • 5.6.1.1.1. Examples
      • 5.6.1.2. MathMorphoMask
        • 5.6.1.2.1. Examples
• 6. Gallery of Examples
  • 6.1. Template creation
  • 6.2. fMRI spatial preprocessing
  • 6.3. Functional connectivity