As long as the images are not resliced, they are still in the same voxel 
space and therefore the same transformation is necessary (which is 
estimated by realign). Therefore you will get always the same 
realignment parameters as long as the realignment works well. But if the 
starting condition for the estimation is wrong (big jump between two 
images), the estimation may run into a wrong local minimum. By changing 
the start conditions (manually reorienting the images), this can be 
improved.

Hope this helps,

Michael

Am 03.07.2014 17:41, schrieb Anjanette P Harris:
> Marko - thanks for your comments/ help with this.
>
> Manually reorienting the images does change the images - I can check reg
> and see that they are roughly aligned, but then running realignment
> seems to ignore the changes and they are not aligned anymore.
>
> One thing you said that worries me - Can I clarify, when I coreg my mean
> functional to my structural, I do not select the other functionals as
> "other" images.  My preprocess batch for my rat fMRI data is :
>
> - realignment:est and reslice (mean only);
> - cogreg: est (ref image the mean functional, and source image
> structural, other images blank - because the mean image is in alignement
> with - the other functionals and the structural is jiggled to match this);
> - segment coreg images ie the structural;
> - normalise: write (segment params to realigned images, ie the
> functionals);
> - smooth;
> -  normalise params written to structural image.
>
> Is this sounding sensible? it is the above processing that I have to run
> twice to get some data to line up...
> thanks again,
> A
>
>
>
> On 03/07/2014 12:29, Marko Wilke wrote:
>> Hello,
>>
>> looks like I started this, so...
>>
>>> 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.
>>
>> I am still under the impression that, if you use spm to display your
>> images, you should see a difference in the orientation after
>> realignment (potentially play around with voxel and world space, but
>> it should be visible). It may not be that obvious but one way to find
>> out whether anything happened at all to the images is to check the
>> timestamp of their last modification (that is one reason why I still
>> like img/hdr combination, you can tell much easier :)
>>
>> Also, what I meant is when doing "coreg mean to structural", you have
>> to specify all other EPI images from this run as "other" images. This
>> is where I have repeatedly failed to do the obvious myself, hence my
>> warning to check that this actually happened. Again, time of header
>> modification is one way to be sure.
>>
>>> 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.
>>
>> Not sure this is correct but theoretically, if you rotate all images
>> in one run in an identical way, the difference between them, and what
>> it needs to register them on top of each other, will not change. This
>> would be one explanation, another could be that the realignment
>> procedure uses the original orientation which may still be encoded in
>> the header somewhere.
>>
>>> One suggestion I had was to use cogregister to put the functional in
>>> alignment - but this did not work.
>>
>> You mean you ran coreg, estimate on all images individually, with
>> image 1 as the reference? That should work, albeit it seems a bit
>> cumbersome and may not be as good as simple realignment as it is
>> mainly meant for between-modality matching.
>>
>>> 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?
>>
>> If you do not reslice, my only concern would be that it should not be
>> necessary, and that I would rather like to know where the underlying
>> problem is.
>>
>> Not sure this helps but I think I am going to leave it at that.
>>
>> Cheers,
>> Marko
>
>

-- 
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Dr. Michael Erb
Department of  Biomedical Magnetic Resonance
University of Tübingen
Hoppe-Seyler-Str. 3
72076 Tübingen, Germany
Tel.: +49(0)7071/2987753    priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
e-mail: <[log in to unmask]>
www: 
http://www.medizin.uni-tuebingen.de/Forschung/Kliniken/Radiologie/Biomedizinische+Magnetresonanz.html
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