Dear Patricia,
I am having exactly the same problem as you! I am scanning rats and some
of them managed to rotate around slowly during the scan - when I run my
preprocessing (realign, reslice only mean image, coreg mean to
structural and then normalise and segment to template) I find that the
functional scans are still rotated round by the end of the scan. Like
you, I tried to use reorient to put the functional scans roughly in
alignment , but when I ran realign etc again the motion curves were
identical as if I had not reoriented the images and they were all still
rotated by the end.
One suggestion I had was to use cogregister to put the functional in
alignment - but this did not work.
The only thing that worked was to run my preprocessing twice. But is
this a good idea? I have no idea, I only know that now my scans line up
nicely. Could someone tell me why running realign etc twice is not a
good idea?
Anjie
On 30/06/2014 14:50, Patricia Romaiguère wrote:
> 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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