Hi,
I don't think you should be padding or merging or anything like that.
The registration should take care of problems where there are displacements in the image, even when things go out of the FOV. So I think the important thing to concentrate on is trying to fix your registrations. How are you running them at the moment? And do you have good brain extraction?
All the best,
Mark
On 12 Aug 2013, at 22:31, "Grossman, Yael" <[log in to unmask]> wrote:
> I'm not trying to pad or change directions. The problem is that the starting slice is not the same bregma for all my images. Thus, Image file 1 will have, say, bregma 2 for brain slice 2 in the image, but image_file2 will have bregma 3 for slice 2 in the image. So I need to align the images which are off so that they have the same bregma for the brain slice so that they can align properly when I average. If I can't, then I may just have to exclude the amimals which are off.
>
> I'll try removing each slice then merging.
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of wolf zinke [[log in to unmask]]
> Sent: Monday, August 12, 2013 3:47 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
>
> Hi,
>
> I am not entirely sure if I understood you correctly. But a few comments.
>
> You say that you try to create a templatewith flirt iterations - do you
> upsample the template and use the higher resolution image as reference
> for subsequent iterations? This might help a bit.
>
> Regarding the slice padding, it might be possible to extract a single
> slice with fslroi, zero it with fslmaths, and than pad it again with
> fslmerge, using the option for the correct dimensions. Just make sure,
> that the header remains unchanged, i.e. that the origin is the same in
> the padded and unpadded volumes.
>
> I hope this helps,
> wolf
>
> On 12/08/13 19:01, Yael Grossman wrote:
>> Hi,
>> I don't know if this is possible to do in FSL, or if it's possible at all.
>>
>> I'm analyzing fMRI images from a mouse study and somehow, during the imaging process, the brains became misaligned. What this means is that for some fMRI images slice 2 would be bregma 2, but for others slice 2 would be bregma 3. Since there is no mouse brain atlas, I'm trying to average the brains through a series of FLIRT iterations, but this misalignment really warps the averaging. I was wondering if there was a way in FSL that I could change the image in slice 2 to now be in slice 3 so that the brains are more aligned and the averaging won't give me ghost images.
>>
>> If anything about my problem is unclear, please tell me and I'll try to explain it better.
>>
>> Thank you,
>> Yael
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