Issue Creating Image of Excluded Gradients

[ajdneuro]

Hello, I am getting the follow error at the end of running dMRIprep when writing the excluded gradient file. Do you have any suggestions for avoid the error:

CreateImagesOfExcludedGradients [2023-08-01-14-01-46] axial_image = self.AxialView(iter_gradients, input_size, input_image) [2023-08-01-14-01-46] File "/hpc/software/DTIplayground/0.4.1/lib/python3.9/site-packages/dtiplayground/dmri/preprocessing/modules/QC_Report/QC_Report.py", line 282, in AxialView [2023-08-01-14-01-46] extracted_slice = slice_extractor.Execute(input_image) [2023-08-01-14-01-46] File "/software/DTIplayground/0.4.1/lib/python3.9/site-packages/SimpleITK/SimpleITK.py", line 9508, in Execute [2023-08-01-14-01-46] return _SimpleITK.ExtractImageFilter_Execute(self, image1) [2023-08-01-14-01-46] RuntimeError: Exception thrown in SimpleITK ExtractImageFilter_Execute: /tmp/SimpleITK/Code/Common/include/sitkTemplateFunctions.h:96: [2023-08-01-14-01-46] sitk::ERROR: Unable to convert vector to ITK type [2023-08-01-14-01-46] Expected vector of length 4 but only got 3 elements. [2023-08-01-14-01-46]  [2023-08-01-14-01-46] [Pipeline.runPipeline] Processed time : 11861.58s

[scalphunters]

It happens usually when the input is nifti, which I suspect simple ITK's IO issue (failed to read 4d image and reads 3d image only, it's not happening for nrrd). To clarify, was your input NIFTI? And what version of dtiplayground did you use?

[ajdneuro]

Hello, thanks for your quick response! Yes the inputs are .nii.gz? Would converting to .nii fix it or should I convert to .nrrd?

Best, Alex

[scalphunters]

I've tried converted NRRD, and it worked ok for me. Pls kindly report when it doesn't work. You can convert nifti to nrrd with dmriprep (IDENTITY_Process with different output format (nrrd))

[scalphunters]

closing this issue, pls reopen if anything like this happen again.