Thank you, Mark! Yes, this was our first fMRI experiment ever and we trusted our scanner expert a bit too much in the design. We're not even completely sure if it will be possible to get ANYTHING from this data, but we hope that it may at least be good enough for us to get something preliminary that will indicate if this is an avenue of analysis that we should pursue.
Of course if we do pursue it, we will have a MUCH different scanning design.
Thank you again for all of your help. I'll try fslmerge and nudge to reassemble slices.
Best,
Yael
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Saturday, August 17, 2013 4:18 AM
To: [log in to unmask]
Subject: Re: [FSL] Possible to change arrangement of slices in FSL?
Hi,
I now have a better understand of this problem. These images will be really, really difficult to register accurately because your through-slice voxel dimension is **ten times** the size of your in-plane voxel dimensions, which is an absolutely massive anisotropy, and you loose almost all useful detail in the through-slice direction. Therefore I doubt there is a registration solution that will work here with images like these. I would strongly advise you to try and get less anisotropic images in the future.
For the moment you are probably best off trying to do things manually wrt the slice start and end positions, as I think you already started to do. You can use fslroi to crop images and fslmerge to reassemble slices, if necessary. Alternatively, you can try the Nudge tool to manually put things into a closer alignment.
Sorry I don't have better news, but I just don't think that the quality of these images is sufficient for any accurate registration.
All the best,
Mark
On 16 Aug 2013, at 18:02, "Grossman, Yael" <[log in to unmask]> wrote:
> 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.
> ________________________________________
> 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
> ________________________________________
> 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
