Hi Bruce,

thank you very much!

Brigitte

2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Brigitte,

could you cc the list so that others can answer? I'm not sure what qualifies as "turned around" in FSL. They may have some preferred oreintation. In general we don't, and as long as the direction cosines are preserved (i.e. avoid analyze format!) you should be fine

Bruce

On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Bruce,

...

thank you very much! Please excuse a (potentially naive) follow-up question (as we didn't use external markers): So if in FSL some raw T1 data are found to be "turned around", is it something that Freesurfer "takes care of" at a certain point in the analysis or would you suggest to swap/correct the data after checking w/ FSL and then analyze them with Freesurfer?

Thanks again and kind regards! Brigitte

2013/6/19 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Brigette,

  not sure how you could do this except visually. Bring the images
  up and verify that the directions that we specify are correct
  (although of course this isn't possible for L/R unless you have
  some type of external fiducial marker like a vitamin E tablet)

  cheers
  Bruce
  On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

        Dear Freesurfer experts,

        is there a command in Freesurfer to check for
        correct orientation (LAS vs.
        PSR) of T1 images (similar to "fslhd" in FSL)?

        Thank you very much!
        Brigitte

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