Issue Converting Eddy-Corrected Nifti Files to MIF Format Using mrconvert

Hello Mrtrix community,

I hope this message finds you well. I’ve encountered an issue while trying to perform fixel-based analysis using Mrtrix. Specifically, I’m attempting to convert Nifti files that have been preprocessed with FSL Eddy to the MIF format using the following command:

mrconvert $i-eddy.nii.gz $i-eddy.mif -fslgrad $i-eddy.eddy_rotated_bvecs $i-dwi.bval

However, I’ve noticed an unexpected behavior during this conversion. While the conversion seems to work correctly for the first three volumes, the subsequent volumes are being converted as all zeros. I’m puzzled by this outcome and would greatly appreciate any insights the community might have regarding this issue.

I’ve double-checked the input files and their compatibility, but so far, I haven’t been able to pinpoint the exact cause of this problem. Could this be related to some parameter settings or an inherent limitation of the conversion process? If anyone has encountered a similar situation or has any suggestions on how to troubleshoot and resolve this, I would be extremely grateful for your input.

Thank you in advance for taking the time to read my message and for any assistance you can provide.


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