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Pipeline for processing diffusion MRI and recostruncting deterministic tractography according to the requirement of the Neurosurgery Department of APSS Trentino.

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FBK-NILab/APSS-Tractography

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APSS-Tractography

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:

  1. Structural Dicom to nifti
  2. Structural brain extraction
  3. Diffusion DICOM to nifti
  4. Diffusion brain extraction
  5. Eddy current correction
  6. Rescaling isotropic voxel
  7. Registration of structural data
  8. Registration of atlas
  9. Reconstruction of tensor model
  10. Tracking of streamlines
  11. Tractome preprocessing

Dependencies

To Run the Pipeline

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

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Pipeline for processing diffusion MRI and recostruncting deterministic tractography according to the requirement of the Neurosurgery Department of APSS Trentino.

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