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Dear Chris,

As long as the labels are correct (attached to the right bits of anatomy as viewed in FSLView) then it doesn't matter what way around the data is stored.  FSL will be happy with any format.  Just make sure the labels are correct.

All the best,
	Mark


On 17 Aug 2011, at 22:54, Christopher Bell wrote:

> I am interested in converting some data from dicom to nifti and using FSL for subsequent processing, but NOT image-viewing purposes. I am planning to use either dcm2nii or mri_convert. The NIFTI-1 data displays appropriately in freeview using either conversion tool. Is there anything else I need to do to make the data FSL-happy, or will flirt/feat/melodic/dtifit be able to handle that data and understand L/R S/I and A/P? Or do I need to perform additional fslorient or fslswapdim steps? 
> 
> I did notice that data converted with mri_convert is in RAS format, whereas data converted with dcm2nii is in RAI format, but other than that the images seem equivalent. Would this make any difference as far as FSL is concerned? Thanks for any guidance.
> 
> Chris Bell
>