Hi,
If the .hdr/.img files are actually in the NIFTI pair format, and either the qform or sform information is set (which records crucial information about what is left and what is right in the image) then there is no disadvantage compared to the .nii format. However, if the .hdr/.img pair are in ANALYZE format then that is a problem because the ANALYZE format does not record the crucial information about left/right and so you cannot be sure about this orientation. For that reason we strongly discourage the use the ANALYZE.
You can tell what format the data is in by using fslhd.
This will also tell you if the qform or sform are set (either qform_code or sform_code should be non-zero).
All the best,
Mark
On 19 Feb 2014, at 06:54, Johannes Klene <[log in to unmask]> wrote:
> Hi guys,
> I have a pretty basic question (my first fMRI analysis), but I can't seem to find a straightforward answer: what are the advantages and disadvantages of using .hdr/img files versus .nii files in FSL (and which one do you recommend)? My MRI-data is stored as .hdr/img but I've been converting them (with fslchfiletype) to .nii, although I have to admit without good arguments and understanding of the consequences (if any).
> Best. Johannes
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