Hi,
With only the phase map you will not be able to account for any between-scan motions of the subject, but you can still get a good alignment by using the scanner system. Just do this:
flirt -in phase -ref T1 -usesqform -applyxfm -out phase2T1
where you should change the names "phase" and "T1" to match your image names.
This should give you the phase aligned with the T1, and then you can use the T1 as your "magnitude" image.
All the best,
Mark
> On 22 Aug 2018, at 22:22, Julian Macoveanu <[log in to unmask]> wrote:
>
> Thanks, but what can I do about it?
> On Wed, Aug 22, 2018 at 10:08 PM Glasser, Matthew <[log in to unmask]> wrote:
>>
>> That could be the reason.
>>
>> Peace,
>>
>> Matt.
>>
>> On 8/22/18, 1:53 PM, "FSL - FMRIB's Software Library on behalf of Julian
>> Macoveanu" <[log in to unmask] on behalf of [log in to unmask]>
>> wrote:
>>
>>> Hi list,
>>>
>>> I am trying to realign/reslice a T1 image to a fieldmap phase image
>>> for the purpose of fieldmap correction with FEAT (the scanner did not
>>> output the magnitude file just the phase file, so I have to use the T1
>>> instead of magnitude). I also tried the opposite, to register the
>>> phase to T1 and still doesn't work. The phase file is not very
>>> contrasty, could that be a reason or any other ideas?
>>>
>>> Best,
>>> Julian
>>>
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