Sammba-MRI provides easy-to-use pipelines to process and analyze small mammals brain MRI multimodal images. Sammba-MRI will perform automatically several critical steps for MR image analysis.
- Conversion of Bruker DICOM files to NIFTI-1
- Image quality check
- Image registration and creation of a template
- Transformation of individual dataset to the template (or to an atlas)
- Evaluation of cerebral atrophy on the basis of an atlas
- Estimation of cerebral perfusion maps from FAIR EPI images
- Resting state fMRI analysis connectivity and brain images visualization are straightforward with nilearn once the registration is performed.
Sammba-MRI integrates functionalities from a number of other packages (listed under the dependencies section below)
The required dependencies to use the software are the software:
- FSL >= 5.0
- AFNI
- ANTs
- Python >= 3.5
- RATS for brain extraction
as well as the python packages:
- setuptools
- Numpy >= 1.14
- SciPy >= 0.19
- Nibabel >= 2.0.2
- Nilearn >= 0.4.0
- Sklearn >= 0.19
- Nipype >= 1.0.4
If you are running the examples, matplotlib >= 1.5.1 is required.
If you want to run the tests, you need nose >= 1.2.1 and doctest-ignore-unicode.
If you want to convert DICOM files to NIFTI files, you will need the DICOM ToolKit (DCMTK) package
Sammba-MRI source code can be downloaded with the command:
git clone https://github.com/sammba-mri/sammba-mri