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Hi Mariam, I'm having trouble finding anything wrong with your second level analysis (.gfeat) results - it all seems to line up with the first level .feat results. Can you clarify exactly which image(s) you were looking at that were incorrectly oriented, and how you were viewing them? Thanks, Paul On Wed, Feb 11, 2015 at 6:17 AM, Mariam Sood <[log in to unmask]> wrote: > Hi Paul, > > I have uploaded the folders (Mariam-FSL.zip) to the URL. There is a Readme > in it mentioning anything non-standard I have done. > Much appreciate your help. > > Many thanks, > Mariam. > > On 10 Feb 2015, at 16:36, paul mccarthy <[log in to unmask]> wrote: > > Hi Mariam, > > Could you please upload your .gfeat folder, and one of the first level > .feat folders to this URL? > > https://oxfile.ox.ac.uk/oxfile/work/extBox?id=214687855CEEB78A7E > > Thanks, > > Paul > > On Mon, Feb 9, 2015 at 3:41 PM, Mariam Sood <[log in to unmask]> > wrote: > >> Dear FSL experts, >> >> I am doing a partial post-stats analysis to my data. I had selected ‘Copy >> original FEAT directory for post-stats/registration’ in the misc tab. I did >> not want to loose my original registration, hence turned off the >> registration. Post-stats works fine (during the process of backing up, the >> software was complaining about a few missing files such as design.lev which >> is never in my FEAT directory. I worked around the problem by creating >> dummy files). After post-stats, individual run’s FEAT results looks fine. >> >> Next I did a GFEAT using the newly created FEAT folders, and there seems >> to be something not right with the registration. The new GFEAT folder >> doesn’t seem to have inputregs folder, and the data is oriented in the >> opposite way. If I look at the GFEAT results using my original >> registration, what should be seen at the occipital lobe is at frontal lobe >> and vice versa. >> >> I tried to edit design.fsf files in the new FEAT folders (after >> individual runs were processed) to suggest that they had gone through >> registration, hoping GFEAT process is looking at the registration settings >> in these files, but that does not seem to fix the problem. >> >> I am happy to edit any settings in the files rather than redo >> registration. >> >> Please advice. >> >> Many thanks, >> Mariam. >> >> Mariam Sood >> PhD Student. >> Birkbeck, London. > > > >