Hi Mark!
Thanks for your questions! I am not sure of the cost function I'm using,
I think it is default? I am starting nearly aligned as far as I can
tell, this is just because we take the ASL and T1 scans very close
together, and as such hope that the images should be fairly closely
aligned to start with, barring movement. However, does this mean that in
FSL the images will stay closely aligned? I cannot load the ASL and
mprage together because of the dimension mismatch.
Is there a specific cost function that you would recommend? In
'advanced options' it says 'correlation ratio'.
Thank you!
John Kuster
> Hi,
>
> What cost function are you using?
> Have you tried different ones?
> Also, do you start nearly aligned or in
> quite different orientations?
>
> All the best,
> Mark
>
>
> On 1 May 2009, at 16:50, John Kuster wrote:
>
>> Hello Hedok,
>>
>> Our slices are about 5mm thick, 3.5x3.5 voxes, for 16 slices,
>> partial
>> field, with no gap, but I have to check on the gap, it may be 1mm
>> because of constraints.
>>
>> Flirt basically worked well for most of our subjects, but failed
>> for a
>> few. Do you think the resolution differences combined with the partial
>> field may be putting flirt on the threshold of failing? I have tried
>> cleaning up the ASL scans by cropping the background using bet with
>> f=.2. This helped for a few, but not for the worst ones. Then, I
>> tried masking the original image and the result was similar with the
>> same few failing.
>>
>> I am basically at a loss as to how I can get flirt to work a little
>> better.
>>
>> thanks for your input!
>>
>> Jake
>>
>>
>>> Dear John,
>>>
>>> Just curious about your ASL(arterial spin labeling) image parameters.
>>>
>>> Do you acquire them with very thick slice(~7mm) with gap ~1mm?.
>>> Is this partial or full brain coverage?
>>>
>>> I don't have much experience in ASL, but I remember it was quite
>>> difficult to even coregister anatomical with perfusion weighted
>>> image.
>>> Let me know how it goes.
>>>
>>> Hedok
>>>
>>> Jesper Andersson wrote:
>>>> Dear John,
>>>>
>>>> just to add to Matt's previous comment.
>>>>
>>>>> I tried to run the following command,
>>>>>
>>>>> Command:
>>>>> fnirt --ref=swap_CTRL02_T1.nii.gz --in=swap_CTRL02_ASL.nii.gz
>>>>> --aff=CTRL02_ASL2T1_auto1.mat --cout=CTRL02_ASL2T1_auto2.mat
>>>>
>>>> From the names of your --ref and your --in file I am guessing you
>>>> are
>>>> trying to register a subjects ASL scan to the same subjects
>>>> T1-weighted structural scan. Is that correct?
>>>>
>>>> If so there are two issues:
>>>> 1. Since it is the same subject you really only need 6 dof, i.e. all
>>>> you need to do is to make sure the images are in the same
>>>> "position".
>>>> 2. The contrast in an ASL image is very different from that of a
>>>> T1-weighted image, something that fnirt would struggle with.
>>>>
>>>> Both these issues suggest that what you really need is flirt, and
>>>> that
>>>> will run just fine on a 32bit machine.
>>>>
>>>> Good luck Jesper
>>>
>>>
>>>
>>
>
>
>
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