I have no experience with it, but have you tried using rBET to avoid
having to do them by hand?
http://www.kcl.ac.uk/iop/depts/neuroimaging/research/imaginganalysis/Software/rBET.aspx
On Tue, Aug 13, 2013 at 7:37 PM, Grossman, Yael <[log in to unmask]> wrote:
> Hi Mark,
>
> I'm doing the brain extraction by hand (because the FSL webpage said that BET doesn't work so well on animals and children, and these are mouse brains). I wasn't the one running the fMRI scan- my institute has someone who is in charge of animal fMRI scans and I'm not sure of all the specifics. I know that he was running them with a TR of 3 seconds and a slice thickness of 1.3 mm.
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Tuesday, August 13, 2013 5:00 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
>
> 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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Niels Bergsland
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