Hello all, 

I am new to the DKI preprocessing using MRtrix/fsl and I am encountering a challenge with my dataset.

Specifically, my collected data consists only of three files: *.nii, *.bvec, and *.bval. 
PS: I do not have PA or AP phase-encoded image files included.

In my preprocessing workflow, I have employed the following commands:

 

mrconvert -fslgrad HC001_preop.bvec HC001_preop.bval HC001_preop.nii HC001_dwi.mif
dwidenoise HC001_dwi.mif HC001_den.mif -noise noise.mif
dwiextract HC001_den.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
mrcalc HC001_dwi.mif HC001_den.mif -subtract residual.mif
mrdegibbs HC001_den.mif HC001_den_unr.mif

 

However, I am encountering difficulty with the "dwifslpreproc" command.
I would greatly appreciate your guidance on how to proceed with the preprocessing in the absence of the phase-encoded files? Could someone please assist me in navigating this issue?

Hi there,

We have a program called PyDesigner (https://pydesigner.readthedocs.io/en/lat...) that performs all the same pre-processing and also provides tensor calculations for diffusion and kurtosis along with their associated rotationally invariants (MD, FA, MK, etc). It is written entirely in Python and easily installed in a 'conda' environment. It could be a good solution as it automatically checks and runs the correct commands for the given data. It also can take in the DICOM folder as input. There is a tutorial video at the URL I posted above. There is also a GitHub forum for issues if you run into trouble (https://github.com/muscbridge/PyDesigner). The outputs are also compatible with MRTrix (orientation-wise) and FSL commands. 

Hope this helps, let us know. 

Best regards,

-Hunter Moss

Thank you for your reply. I think the video tutorial is very helpful.

I tried running the tool on my data. The dataset does not have encoding direction. I have 4 files:
1. Image file .nii, 2. .bval file, 3. bvec file and 4. *.json file.

I installed Pydesigner but I ran in the following error:

pydesigner --standard -o /mnt/hgfs/try/DKI/HC1/ /mnt/hgfs/try/DKI/HC1/T20160603170653_NTang^jia-yu_S19.nii

mrconvert -quiet /mnt/hgfs/try/DKI/HC1/dwi0.mif /mnt/hgfs/try/DKI/HC1/working.mif
[WARNING] Given DWI is partial fourier, overriding --degibbs; no unringing correction will be done to avoid artifacts.Use the "--adv" flag to run forced corrections.
Traceback (most recent call last):
  File "/home/abhishek/mrtrix3/bin/dwifslpreproc", line 1327, in
    import mrtrix3
  File "/home/abhishek/mrtrix3/bin/mrtrix3.py", line 84, in
    if not imported (os.path.join (os.path.dirname (build_path), 'lib')):
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/abhishek/mrtrix3/bin/mrtrix3.py", line 33, in imported
    spec.loader.exec_module (module)
  File "", line 936, in exec_module
  File "", line 1073, in get_code
  File "", line 1130, in get_data
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/hgfs/try/DKI/HC1/lib/mrtrix3/__init__.py'
Traceback (most recent call last):
  File "/home/abhishek/anaconda3/envs/mri/bin/pydesigner", line 8, in
    sys.exit(main())
             ^^^^^^
  File "/home/abhishek/anaconda3/envs/mri/lib/python3.11/site-packages/designer/pydesigner.py", line 646, in main
    mrpreproc.undistort(input=working_path,
  File "/home/abhishek/anaconda3/envs/mri/lib/python3.11/site-packages/designer/preprocessing/mrpreproc.py", line 469, in undistort
    raise Exception('dwifslpreproc failed, please look above for '
Exception: dwifslpreproc failed, please look above for error sources.

Does anyone know what this error represents ? 
Thank you in advance.

Regards,

Abhishek