DICOM 2 NIfTI converter

Convert DICOM files to NIfTI format using different tools.

Input:

• Input images (can be the output of a prior analysis)
• Optionally choose between multiple tools to for the conversion.

Operation Mode:

1. Prepare heading for report.

For each input file:

2. Download 

3. Check type of file - if not nifti, dicom or .raw give error. If it's MRI related, upload it (i.e., b-values, gradients, nii, ...)

Next steps only for DICOM images:

4. Convert to jpeg syntax - To be able to see it easily.

5. Apply sequentially the different converters. If one fails it jumps to the next one.

• dcm2niix -> mrtrix -> dcm2nii -> mcverter -> diffunpack -> ERROR
• A new setting was included to avoid this behaviour if required.
• See info pages of each converter - https://github.com/rordenlab/dcm2niix 
• Multiple dcm2niix versions available:
  • v1.0.20230411 
  • v1.0.20220720 
  • v1.0.20211006 
  • v1.0.20201102
  • v1.0.20190902 
  • https://mrtrix.readthedocs.io/en/latest/reference/commands_list.html 
  • https://people.cas.sc.edu/rorden/mricron/dcm2nii.html 
  • http://manpages.ubuntu.com/manpages/cosmic/man1/mcverter.1.htm 
• If the converter is successful, upload the nifti image.
• All of them distinguish between DW images and not DW images because that data is arranged differently. It also depends on the manufacturer and software version, that's why there are multiple exceptions.

6. If DWI (DWI, HARDI, DTI, DSI) - look for gradients information, b-values, gradient directions.

7. If required - reorient (register) images to MNI space.

8. Upload images and report.

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