Hi,
One thing that can often cause these sorts of smeary artifacts is when
the edge voxels in the
fieldmap are quite noisy. The masking in FEAT uses BET on the
magnitude images, and
that often helps when simple thresholding of the magnitude images
includes too many
non-brain voxels where the phase estimation is poor. So have a look
at your fieldmaps and
if they have noisy voxels at the edge, use BET or change the settings
on your existing
BET to make a tighter mask. This has a much more dramatic effect than
small misregistrations.
All the best,
Mark
On 4 Apr 2008, at 20:21, Doug Greve wrote:
> Drift can cause misregistrations. Is the smearing less on
> functionals collected in close proximity to the B0 maps? Not sure
> why 8 channel would be worse than a single channel (we run it on 8
> and 12 channel).
>
> doug
>
> Adrian Koziak wrote:
>>
>> Great thanks! I'll give it a go. The scans were set up in the exact
>> same
>> imaging locations, but there may be slight misregistrations. I've
>> used an
>> early version of this software, but it may help!
>>
>> It is perplexing, however, that the single channel works fine via my
>> methods, by the 8-channel does not.
>>
>> Regardless, thanks very much for the advice!!!
>>
>>
>>
>>
>>> I think that the smearing may be due to misregistration between
>>> the B0
>>> map and EPI. I think that the "ucsd script" that you are using may
>>> be a
>>> modification of my script (epidewarp.fsl). If so you might want to
>>> try
>>> the original as I have been using it successfully on both Siemens
>>> and GE
>>> data. It is distributed with FreeSurfer, but I've put a copy here:
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>>>
>>> This is just a wrapper around fugue and flirt developed as a tool
>>> for
>>> the fBIRN projects (www.nbirn.net).
>>>
>>> doug
>>>
>>>
>>> Adrian Koziak wrote:
>>>
>>>
>>>> Well, after looking at the actual data in the base directory of
>>>> the feat
>>>> anayslis, it seems as though my data does not have the smearing
>>>> shown in the
>>>> results of the prestat analysis (attached). I guess that feat
>>>> applies a mask
>>>> to the data, to get rid of the smearing effect.
>>>>
>>>> Does anyone know if this is correct ???
>>>> Also, is this an acceptable result ???
>>>>
>>>> Thanks very much for everyones input
>>>>
>>>> I've also attached a before and after screenshot of the unwarping.
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> [log in to unmask]
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> In order to help us help you, please follow the steps in:
>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>>
>>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [log in to unmask]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
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