I was planning to use the field map images, but just I looked into it, and unluckily there is no signal in the mouth region so it is not useless ;(
What images are you planning to use to do this? Does your field map or
phase reversed spin echo images actually cover the mouth? Keep in mind
that the black hole in the mouth is not going to come back (though the
tissues of the mouth might otherwise have their positions corrected some).
On 8/7/17, 1:50 PM, "FSL - FMRIB's Software Library on behalf of John
anderson" <[log in to unmask] on behalf of
[log in to unmask]> wrote:
>Dear Dr Matt,
>Thank you very much for the detailed explanation and the suggestions...
>very helpful! I highly appreciate your response!!
>Kindly, I have one additional question:
>In order to run topup on a T1 images I need for feed the acquisition
>parameters as a text file to the flag detain.
>Kindly how can I get these acquisition parameters? I know it is in the
>DICOMs header, but which tags are relevant to the flag detain? Is it Echo
>Time, Repetition time ..etc ?
>That is predominantly signal loss, from either air in the mouth or metal
>as your T1w image is a gradient echo sequence. While there likely is some
>distortion along the readout direction, it is much smaller than typical
>phase encoding direction distortion as in EPI. You can still correct for
>this with a field map (or a field map computed from topup) as the HCP
>Pipelines do. Theoretically you could even reverse the readout direction
>and run topup on the opposing high resolution images, however in practice
>this is very slow as topup is not optimized for high resolution images and
>also we found issues with fat shifting into the brain with a reversed
>readout direction when we played around with this in the HCP Piloting. If
>you want images of the mouth without dropout you would be better off using
>a spin echo sequence like the Siemens T2w SPACE sequence, though you might
>also need to use something like a bite bar to keep people from moving
>their mouth during imaging.
>On 8/7/17, 12:59 PM, "FSL - FMRIB's Software Library on behalf of John
>anderson" <[log in to unmask] on behalf of
>[log in to unmask]> wrote:
>>Dear FSL experts,
>>I have T1 images with a "susceptibility-induced distortions" in the mouth
>>area (attached). I am wondering if "topup" works on T1 images. If yes
>>what is the detain file in this case?
>>I appreciate your feedback!