Hi Marko, Helmut and everyone,
Thank you Marko for your answer.
Also thanks to Helmut for sharing is thoughts. I will need a little bit
more time to process them, but they are very welcome. On a much more
practical side, there's a statement in Marko's reply that's got me worried:
>> We tried to move the Time2 time series using the "reorient image" option
>> in checkreg, so they would be in rough alignment with the time series at
>> Time1 before the realign, but found out that as long as the images are
>> not resliced, the realign ignores those changes.
>
> It should not. Have you actually applied the changes to all images?
Yes, I have actually applied the changes to all images. That was my
first thought : that I had not paid attention and done something stupid
(human error is usually a good bet). So I went back to my raw data and
restarted from scratch, this time being extra careful. When I display
the images the Origin and Dir Cos fields are different after the
"reorient images". But when I run the realign, the curves are absolutely
the same whether I reorient the images of the second session or not. I
was so surprised, I tested it a third time on a single subject. I
contacted our MRI analyst who tried and got the same realign curves with
and without reorient. He said it was normal and that the realign would
not take the changes into account if the images were not resliced. I had
been reading the archives and although I don't understand everything, I
did understand that reslicing should be avoided :-) . Hence my question
on the list!
Now if the realign should not ignore the changes in origin and
orientation of the images, I'm worried. I am quite open to the idea that
I'm doing something really stupid, but could there be another reason ?
Has someone ever had the same problem? Or has someone any suggestion on
what we should check for?
Again, thank you all for your help
Patricia
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