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Hi John, thank you for your willingness to help! Here is the zipped image https://www.dropbox.com/s/relsv8gkbkm2qeo/problem.nii.zip?dl=0 Hi Helmut, thanks a lot for the explanation. Yes, it is "the raw data plus the GM TPM to illustrate the raw data having a similar orientation after manual adjustments, with the segmentation output still not satisfying". It would be great if you could take a look at the raw data ( https://www.dropbox.com/s/relsv8gkbkm2qeo/problem.nii.zip?dl=0). Thanks folks! :-) Marris On Sat, May 9, 2015 at 12:55 AM, H. Nebl <[log in to unmask]> wrote: > Or I completely misunderstand you and it's the raw data plus the GM TPM to > illustrate the raw data having a similar orientation after manual > adjustments, with the segmentation output still not satisfying? > > In that case the deviance might still be too large, the raw data would be > around 10 to 15 mm "too high" along z, so you would have to shift the raw > file downward = shift the origin upward. > > If this doesn't solve the issue, please send the raw file (compressed as > RAR or ZIP) or a download link to me, I'll check the file tonight. > > Best > > Helmut > >