I can't report from a lot of experience in that particular case my self, but I think the

• Insight Segmentation and Registration Toolkit , short ITK 

might help you out. See:

• http://www.itk.org/itkindex.html
• http://www.itk.org/ItkSoftwareGuide.pdf

The MIPAV tool box can convert  mha format to nifti and dcm 

Hey Ziba,

If you have ITK just use:

import Skimage.io As Io

path = '$PATH/*.mha' #path to your MHA file

outpath = '$PATH/*.nii'

img = io.imread(path,plugin='simpleitk')

io.imsave('outpath',img,plugin='simpleitk')

if not, first install the necessary ITK wrapping:

pip Install Scikit-image

pip Install simpleITK Or Easy_install-U simpleITK

and then run the other 5 lines ;)

You could do it with Matlab also, check the stackflow/fileexchange on the matlabcentral for some usefull tools ;)  such as: http://www.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d

Hope this helps,

Gabriel

check out this link below,  it might be a help

http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

Clara Framework NVIDIA does, but it is a tool that goes much further than that.