Troubles using built-in volumeViewer() app?

I am converting a series of dicom slices into a single nifti image. To do this I am using a popular software downloaded from the internet, spm12. My goal is to convert the dicom files to the nii format then view them in some image viewer( either Amide, volumeViewer(), etc) to make sure that there raw data matrix has the same orientation and position in space regardless of coordinate system change or any transformations applied to either the nii or dicom files. In order to do this I must know, with certainty, 2 things about the behavior of niftiread,dicomread and volumeViewer:

1. Do niftiread and dicomread return the raw data present in the image OR do they apply any coordinate flip with any transformation from metadata then return the raw data?

2. Same goes for volumeViewer(), does it just take in a data matrix from dicomread or niftiread then display it exactly as it is? Or does it use metadata and know that this data matrix is a nii or dicom image then flip the axis's or apply a transform to it?

Any help on how Amide behaves would also be a bonus!!

I have read the descriptions and parsed through the code of the functions themselves, but having clarity about the behavior of these functions would greatly increase my debugging process.

Any help is greatly appreciated and feel free to comment with questions if this is either wordy and confusing or not descriptive enough.

EDIT: As of right now I'm viewing a dicom image in the volumeViewer() that is 90 degrees rotated about the Z-axis and x and y axis flipped compared to the nii image. The flips makes sense due to coordinate changes, the 90 rotation does not, leading me to believe a issue with the functions. Png image attached for reference.