Incorrect dimensions using Bio-Formats to open .nii and nii.gz NIfTI files

I’ve used dicom2nifti to convert a dicom MRI stack (256x512x36 in xyz respectively) into nifti. I’m trying to use the Bio-Formats plugin in FIJI to view the output nii.gz file (or .nii if I extract first) to verify that it has properly converted my image stack. I’m able to view the input dicoms just fine using the File > Import > Image Sequence tool.

My problem is that when I try to view the output nifti, either with the built-in import options or with Bio-Formats, the image is either a corrupted mess of static or the dimensions are swapped to 36x256x512 (rather than 256x512x36).

I have tried changing the bitness, signed/unsigned, and endianness using the standard import tool, and with Bio-Formats I have tried the different stack viewers and the “Swap dimensions” option (and most other checkboxes), but nothing seems to work. I am particularly confused by the “Swap dimensions” option, because it only allows me to change Z, C, and T rather than X, Y, and Z, and it only lets me choose between 1, 1, and 512, rather than my actual pixel dimensions. I’m fairly certain that I used the dicom2nifti conversion tool correctly and that the issue is with me using FIJI correctly to view the result.

Thanks in advance.

Hi @caligos, are you able to share the file to a public location so that we can test it? (If you dont have a suitable upload location we would recommend Zenodo)

Hi @dgault, sure I will try to upload to Google Drive or maybe Zenodo, but I need to verify that all patient info/metadata has been removed first. I’ll reply again here when I’m done.