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minor typo no ?
Before: self.root_dir, nifti_file_name) for nifti_file_name in nifti_file_names if nifti_file_names.endswith('.nii')]
After: self.root_dir, nifti_file_name) for nifti_file_name in nifti_file_names if nifti_file_name.endswith('.nii')]
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There are a typo and a missing line that prevent the workflow for own datasets to work.