Hi,
It sounds like your registrations are failing for some reason.
The red lines indicate edges taken from one image (e.g. structural)
and overlayed on the greyscale for the other image (e.g. functional).
There should always be red lines and they should align with the
visible structures in the greyscale images.
I would investigate this problem by looking at the images in
the reg subfolder of the feat directories. The example_func image
is the original functional image (one volume out of the series).
Check if this is oriented the same way in the original 45 cases
and the subsequent ones.
Also check the "highres" image as this is the structural image
for each subject. Again, see if there is a difference in the first
45 and the others.
Finally, check the image "example_func2highres" and "highres2standard"
as these represent the registered image outputs. In the first
case it should align well with the highres (load both into FSLView)
and in the second case it should align with the standard image
(again, load both into FSLView).
More information on registration and these outputs can be found
in the documentation and the FSL course practicals.
All the best,
Mark
On 17 Aug 2010, at 18:33, Joseph P. Lowinske wrote:
> Hi,
>
> I am currently running a subject-level anaylsis with FEAT across 99
> subjects. When examining the logs of the analyses there are two
> things that appear odd in the registration:
>
> 1) after (roughly) subject 45, the orientation of the brain in the
> registration of example_func to highres switches (in order) from
>
> 4 sagittal slices- 4 coronal slices - 4 axial slices
>
> to
>
> 4 coronal slices (rotated 45 degrees, as viewed in FEAT display) - 4
> axial slices (rotated 45 degrees) - 4 sagittal slices (rotated 90
> degrees)
>
> 2) in roughly half of the post-subject 45 analyses, the registration
> of example_func to highres lacks any red outlining whatsoever.
> Frankly, I do not know what the outlining indicates but, as with the
> issue 1 above, I am wondering if weither of these developments
> represent an issue in our analysis (either at the subject level or
> in the final analysis)?
>
> --Joe
>
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