Siemens dicoms converted with dcm2nii

1. If you convert Siemens dcm using dcm2nii, you need to fix the conversion you need to input:

   >> ni = readFileNifti(yourniftiFile)

in MATLAB to check whether some parameters have the correct dimensions. In particular freq_dim, phase_dim,slice_dim, slice_start and slice_end. If values of these items are 0, you need to modify them, which you can refer to in the nifti standard.

After you change these values, remeber to write back these changes to your nifti files with the command

>> writeFileNifti(ni).

2. A preferred way to solve this issue is to try other tools. Some find dinifti and MRIConvert to perform well.