Nifti files are used by FSL. With extension .nii or .nii.gz
Convert .nii <-> .nii.gz
nii.gz are simply gzipped .nii files, which are smaller in size. Sometimes you might want to convert between them. Simply run
to convert nii -> nii.gz; and
for nii.gz -> nii
The most reliable dicom to nifti converter is dcm2nii, as it works with GE scanner headers correctly.
It's important to check image orientation after file conversion.
fslswapdim will do this.
check header information with mrinfo (MRTrix) or mri_info.