# Outputs

- **Nifti_Trakte**: Contains all manually drawn masks created with DSI Studio.
- **Nifti_Trakte_registered**: Contains the masks registered to our in-house MRI template (MTPL). This registration was performed manually using `reg_aladin` and `reg_resample`.
- **affineTrafo.txt**: This is the output transformation matrix generated by `reg_aladin` during the registration of the `C57BL6_mouse.iso.nii.gz` file to the `NP_template_sc0.nii.gz`.
- **C57BL6_mouse.iso_registered.nii.gz**: This is the output image created by `reg_aladin` when registering the `C57BL6_mouse.iso.nii.gz` file to the `NP_template_sc0.nii.gz`.
- **Nifti_Trakte_V2**: These are the updated tracts (NV).
- **Tract_Density**: This folder contains the density of each generated tract mask, saved from DSI-Studio.