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Manish,

Though dcm2nii can be very fast, some versions on the MAC write the NIFTI magic word backwards in the output header.  This may or may not have changed in the newest release.  A symptom of the problem, if present, is that FSL can read the output NIFTI file but will not display the orientation characters, and SPM may not be able to read the file at all.  If the output file byte positions 344-347 contain the characters "\0 1 + n" you can overwrite them with the appropriate "n + 1 \0" using the unix dd command, thus solving the problem, allowing FSL to display the orientation characters and SPM to read the file.

Kathy Pearson