in matlab easiest is using load_untouch_nii/save_untouch_nii (http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image/content/load_nii.m) and just set the extensions as you want the conversion. Same applies if you use the image calculator of spm, set the file extensions as you want the conversion to run and just put 'i1' as formula.
You could also try downloading the program MRIcron (http://www.mccauslandcenter.sc.edu/mricro/mricron/) which is useful for many things, including having a GUI to convert between file types.
Any AFNI program will convert between Nifti (nii) and Analyze (hdr/img) format. You can really use any program you want, and indicate in the "-prefix" option the format you prefer by adding an extension, ".nii" for Nifti and ".hdr" for Analyze. For example:
3dcalc -a NiftiInput.nii -expr 'a' -prefix AnalyzeOutput.hdr
3dcalc -a AnalyzeInput.hdr -expr 'a' -prefix NiftiOutput.nii
Try out MRIConvert 2.0
http://lcni.uoregon.edu/~jolinda/MRIConvert/
It is easy to use and quite convenient in converting many images in a quick and orderly way.
fsl5.0-fslchfiletype NIFTI_PAIR input_filename.nii.gz &
OR
fslchfiletype NIFTI_PAIR input_filename.nii.gz &
Pretty straightforward and amenable to scripting.
Tested on Ubuntu 12.04 x64/FSL 5.0.6
Besides MRIcro, you can also use another itk-SNAP free software to convert hdr (img) to nifti images or convert back.
After you install the itk-snap software, you just open the nifti image, then save it as analyze format.
I find following tools for easiest/fastest conversion
http://imagej.nih.gov/ij/
In addition to the suggestions above, FreeSurfer can do this using the the mri_convert command
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