The whole image is inverted in the result of the dcm2nii.gz conversion about dcm2niix HOT 3 CLOSED

I do not have access to a dataset to replicate nor do I use Slicer3D, so this is my best guess. I think this just reflects that NIfTI and DICOM have different spatial coordinates. Specifically, NIfTI uses RAS while DICOM uses LPS. To test my hypothesis, drag and drop your NIfTI file on the NiiVue live demo and ensure the (L)eft, (S)uperior and (P)osterior text is correct.

from dcm2niix.

I found that turning the results directly with the parameters didn't turn out in the right direction, and I'd like to tweak them in bulk, but I don't know how to write the parameters to batch.

the args used to convert the dicom to nii

the converted nii with error orientation

the right orientation by the import > tools > rotation

from dcm2niix.

Hello, I am not sure that the dcm2niix issue board is the correct place for this as you are using bidscoin (a dcm2niix wrapper) and MRIcroGL. However, I will try my best. Many quadruped scans have errors in terms of defining the patient position, and different templates use different rotations. This may require you to rotate the NIfTI spatial transformation to match your desired orientation. When you run MRIcroGL from the command line and choose to re-orient an image, you will notice it will provide the permutation required to the columns, rows and slices to get them to match the NIfTI identity matrix:

Reorient Dimensions -1 3 -2

You could always use this to write a nibabel batch script to adjust the NIfTI affine for a huge number of images that required the same rotation. I am not a nibabel expert, but I think ChatGPT can give you some good hints on how to achieve this.

from dcm2niix.