Thanks to all the GREAT inputs you gave. I will try those and let you know soon.
Best regards
ML
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of John Ashburner
Sent: Mittwoch, 6. Oktober 2010 13:20
To: [log in to unmask]
Subject: Re: [SPM] coregistration
The easiest way is probably to Display the anatomical image, enter various rotations (in radians) and translations (in mm) until the anterior commissure is close to mm coordinate 0 0 0, and the orientation is nicely axial. Then click "Reorient images..." and select the anatomical scan. This will change the matrix in the scan header.
Then Display one of the functional images. Try various rotations and translations until the AC is nicely aligned and the orientation is axial. Click "Reorient images..." and select all the functional scans. This will change the matrices in all the headers of the images you select.
Use the Check Reg button with the anatomical and one of the functional images to see how closely the alignment is.
Repeat as necessary.
Best regards,
-John
On 5 October 2010 16:49, Lloyd STEPHEN Miller <[log in to unmask]> wrote:
> Dear John, can you or someone be a bit more explicit about how to use Display and Check Reg buttons to reorient/position images? We'd like to try this, and are somewhat familiar with "nudging" in other software programs, but not with SPM. We use SPM8.
> Thanks so much! Steve M.
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> On Behalf Of John Ashburner
> Sent: Tuesday, October 05, 2010 6:24 AM
> To: [log in to unmask]
> Subject: Re: [SPM] coregistration
>
> Coregistration can be made more robust by starting with the images in
> closer alignment with each other. The Display and Check Reg buttons
> can be used to change the initial orientation/positioning of the
> images, which reduces the chance of getting stuck in a local optimum.
> The way the algorithm works is to try one set of parameters, see what
> the objective function is and use this to try to get a better set of
> parameters where the objective function is better. Unfortunately,
> doing it this way can result in not finding the best parameters.
>
> An alternative would be to do some sort of grid search. For example,
> trying 20 values for each of the parameters. Unfortunately, there are
> six of them to find, which would make this infeasible. If there were
> two parameters, there would be 20*20 different combinations to try.
> With six there would be 20*20*20*20*20*20 different combinations, and
> it would involve reslicing one of the images 64,000,000 times.
> Therefore, the alternative approach is not really possible.
>
>
> Stripping the skull and nonuniformity correcting the anatomical scan
> can also help. Segmentation can be used to separate brain from
> non-brain, as well as doing the nonuniformity correction. Combining
> the output (grey, white, CSF as well as a bias corrected version of
> the image) can be done using ImCalc.
>
> Best regards,
> -John
>
> On 4 October 2010 22:04, Blefari Maria Laura <[log in to unmask]> wrote:
>> Dear All,
>> I am very happy to decide to join the forum. It seems very active and helpful.
>> My problem is very basic. In my fMRI experiment I am using 20 slices. Can this fact generate problems during the coregistration with the anatomical?
>> I am a little confused about why I got that result (see the attachment).
>> I have been told that I probably need to have a 'peeled' version of my anatomical data. Because it seems that in my functional images, the skull is not visible, making it hard for SPM to coregister the data with the anatomical data, where the skull is visible. Any advise?
>> Thanks in advance,
>> ML
>>
>
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