dancebean/sammba-mri

small mammals brain MRI

sammba-MRI: small mammals neuroimaging with python

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)

Dependencies

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

User guide and gallery of examples are available on

https://sammba-mri.github.io/

Installation

Sammba-MRI source code can be downloaded with the command:

git clone https://github.com/sammba-mri/sammba-mri