OK, I think I have this sorted out now. FreeSurfer can now exchange single-file NIFTI volumes (compressed (nii.gz) and uncompressed (.nii)) with FSL and AFNI. It can exchange single-file uncompressed (.nii) with SPM (still don't know whether spm can do compressed). FreeSurfer can also read two-file NIFTI but not write them. Two-file NIFTI looks like analyze (ie, with .img and .hdr files, but the .hdr is a nifti header).

doug

Doug Greve wrote:

I've just fixed a bug in the way FreeSurfer produces *uncompressed* NIFTI files. It actually always produced *compressed* files, even if the extetion was just .nii and not .nii.gz. I have fixed this, and it will be live in dev tomorrow and live in stable at the next update. I've successfully loaded uncompressed files into both SPM and AFNI, but failed on compressed. Does anyone know if they even can read compressed? Both compressed and uncompressed work with FSL. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting