Sorry, just some information about the files I uploaded. refbrain3 is the composite image after 3 series of FLIRT and averaging. CYT20110627D..._flirtrefbrain is when I tried to register Animal D to the reference brain, Then I have the brains for animals D and C after and bandpass and Gaussian smoothing.
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Grossman, Yael [[log in to unmask]]
Sent: Friday, August 16, 2013 12:42 PM
To: [log in to unmask]
Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
Hi Mark,
I am uploading the images to the website you sent me now. It looks like the problem has more to do with my raw images than registration. If you look at Animal C and D, you will see that slice 1 on C more closely resembles slice 0 on D, while slice 0 on C is more posterior. Since I only have 10 brain slices (a mouse brain with slices in the Z direction of 1.3 mm), this makes a really big difference when it comes to creating a composite image for referencing.
What I would like to do is find a way to change the image file from Animal C so that I can delete everything from slice 0, then shift slices 1-9 down (so that slice 1 is now slice 0, slice 2 is now slice 1, etc). Thus the slices from Animal C will better match the slices from other animals and I can make a better composite reference image.
Thank you,
Yael
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Wednesday, August 14, 2013 2:50 AM
To: [log in to unmask]
Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
Hi,
If you are already using a manual brain extraction then this won't be the problem with your registration.
Can you upload some data to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
in order for us to have a look. Include the images that you are trying to register and a description of how you are going about it.
All the best,
Mark
On 13 Aug 2013, at 18:59, "Grossman, Yael" <[log in to unmask]> wrote:
> Thanks, Niels! I'm not sure if that will work well with my data, but I can't wait to check it out for brain extraction!
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Niels Bergsland [[log in to unmask]]
> Sent: Tuesday, August 13, 2013 1:48 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
>
> 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
>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
> (716) 859-7677
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