DTIPrep

Setting up a new project for DTIPrep processing

DTIPrep expects a project specific protocol file protocol.xml. This ensures the scan collection parameters are the same across scans. The protocol.xml file must be manually created.

1. Start the DTIPrep singularity container in shell mode, with /input directory pointing to a suitable example scan. The /output directory needs to point to a folder with write permission.

   $ singularity shell -B <path_to_input_nrrd_folder>:/input -B <path_to_output>:/output <container>

2. Start DTIPrep in interactive mode.

   Singularity> $ DTIPrep

3. Open NRRD file [image]

4. Navigate to /input and open the example file.

5. On the protocol tab select Default to generate the default protocol. [image]

6. Modify the protocol as required, N.B. capitalisation is important.

• Brainmasking

  If brain masking is required set:

Parameter	Value	Notes
BRAINMASK_bCheck	Yes
BRAINMASK_method	1	Slicer masking

• Dominant direction check

  The dominant direction check looks for artifacts thought to be caused by scanner bed vibration, these are particulary prevalent in older scanners and with smaller subjects (children / animals) ref.

Parameter	Value	Notes
DOMINANTDIRECTION_bCheck	Yes

• Denoising

  If required, it is recomended that only one of DENOISING_bCheck or JOINDENOISING_bCheck is enabled ref.

7. Select Save as and navigate to /output. Save the protocol as dtiprep_protocol.xml.

8. Exit the DTIPrep GUI.

9. Exit the singularity container:

   singularity> $ exit

10. Move the new protocol file to the project metadata folder. `$ mv dtiprep_protocol.xml <path_to_project_metadata>