Dear MRIcroGL developers,

I have an issue with converting my data from DICOM to NIfTI.

I have acquired an isotropic 2 mm DTI dataset and exported it to Siemens mosaic DICOM format. The images were however acquired not in the axial plane but aligned parallel with the base of the skull.

When I converted them to NIfTI, the resulting 4D dataset had the correct pixdims 2 by 2 by 2 (according to FSLeyes), however the transformation matrix is

-1.986      0.118   -0.2023  120.4
0.2251     1.439   -1.37     -89.87
-0.06476   1.384   1.443    -102.5
0              0          0           1

meaning I have actual voxel dimensions of approx. 1.99 by 1.44 by 1.44 so the voxels are squeezed in the y and z directions.

In my other cases when the acquisition plane was plain axial (or aligned to corpus callosum) this error never occurred.

I would like to ask if there is a solution. I also tried to convert the dataset using the older dcm2niigui with the same result.

I will be very grateful for any advice.

Best regards

Samuel