Dear Marina,
I've run your latest images through our default FEAT registration (using the GUI) and they worked perfectly well for me.
Some example images are attached.
I don't know what you are doing that is causing the problems you are having.
Are you using FSL version 4.1.9 ?
Are you sure you are specifying the brain extracted image (that ends with "_brain" in the filename) and that there is also the non-brain extracted image around (same name but without the "_brain" in the filename)?
The problems you are getting look like the problems caused by brain extraction not being correctly used in all images.
All the best,
Mark
On 15 Aug 2012, at 14:33, Marina Shpaner wrote:
> Hello Mark,
>
> To give you a fuller picture, I had run about 40 participants through a script. Each participant has 2 time-points, and I wanted to use the same Fnirt transformation matrix for both time-points. Two participants failed, so I tried the anatomical from the other time point, which also failed. Then I tried the GUI. I just don't understand how this could happen. I now uploaded both participants to 122359.
>
> I really appreciate your help!
>
> -Marina
>
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