Pipeline for processing diffusion MRI and recostruncting deterministic tractography according to the requirement of the Neurosurgery Department of APSS Trentino. At this moment the pipeline includes the following steps:
- Structural Dicom to nifti
- Structural brain extraction
- Diffusion DICOM to nifti
- Diffusion brain extraction
- Eddy current correction
- Rescaling isotropic voxel
- Registration of structural data
- Registration of atlas
- Reconstruction of tensor model
- Tracking of streamlines
- Tractome preprocessing
- NiBabel : http://nipy.org/nibabel , provides read and write access to common medical and neuroimaging file formats.
- Dipy: http://www.dipy.org , provides tools for dMRI data analysis.
- mricron: http://www.nitrc.org/projects/mricron, Toolbox for magnetic resonance image conversion, viewing and analysis.
- FSL: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, provides tools for analysis of FMRI, MRI and DTI brain imaging data.
pipeline.py {<path-to-data>|"number number number"}
For a batch session of analysis all the parameters can be configured in the file parameter.py.
The expected organization of data folder is as follows
- <Subject_Folder> -- DICOM --- Structural --- Diffusion