Hi,
Yes - the FEAT GUI registers the fieldmap magnitude image to the EPI
and then resamples
the fieldmap into the EPI space before applying the correction.
All the best,
Mark
On 26 Jun 2008, at 08:33, Stamatis Sotiropoulos wrote:
> Hi Mark,
> thank you for the answer. Regarding the registration of the
> fieldmaps (question c) prior to the correction of the EPI
> distortion, I would think that the modulus image needs to be
> registered using the EPI as a reference and then apply the
> transformation to the phase images. Is that what the FEAT GUI does?
>
> Thanks again,
> Stamatis
>
>
> ----- Original Message ----- From: "Mark Jenkinson" <[log in to unmask]
> >
> To: <[log in to unmask]>
> Sent: Wednesday, June 25, 2008 11:22 PM
> Subject: Re: [FSL] EPI distortion correction using FUGUE
>
>
>> Hi,
>>
>> a)
>> These commands look just fine.
>> You may want to see if the resulting fieldmap_rads is noisy at the
>> edge of
>> the brain and mask it with a tighter mask (one produced by BET) to
>> get
>> rid of any noisy voxels there.
>>
>> b)
>> You want the phase range to be 2*pi. It doesn't matter if it is 0
>> to 2*pi
>> or -pi to pi.
>>
>> c)
>> As for the fugue line, I would advise doing things using the FEAT GUI
>> (in pre-stats mode) as this applies the registration steps for you,
>> whereas
>> using fugue at the command line assumes that you have already done
>> the
>> registration. Using the FEAT GUI is the way we general recommend
>> performing undistortion.
>>
>> All the best,
>> Mark
>>
>>
>>
>>
>>
>> On 25 Jun 2008, at 21:04, Stamatis Sotiropoulos wrote:
>>
>>> Hi all,
>>> I am using prelude and fugue to correct for EPI distortion. I
>>> have two
>>> modulus and two phase images corresponding to two gradient echo's
>>> with
>>> different TE, and I am using the following command line scripts:
>>>
>>> prelude -a modulus_echo01 -p phase_echo01 -u phase01
>>> prelude -a modulus_echo02 -p phase_echo02 -u phase02
>>> fslmaths phase02 -sub phase01 -div 0.0031 fieldmap_rads -odt float
>>> fugue -i EPI_image --loadfmap=fieldmap_rads --dwell=0.000767 -u out
>>>
>>> where TE=0.0031 sec and dwell_time=0.000767 sec.
>>> a) Is the above sequence correct?
>>> b) The phase_echo images that are used as input to prelude, should
>>> be
>>> scaled in the range 0 to 2*pi or -pi to pi?
>>> c) Should the modulus and phase images be registered first to the
>>> EPI
>>> image? They are acquired just after the EPI acquisition with
>>> exactly the
>>> same field of view and resolution. Or fugue performs this
>>> registration?
>>>
>>> Thank you in advance,
>>> Stamatis
>>>
>>> Stamatios N Sotiropoulos
>>> Clinical Neurology
>>> University of Nottingham, UK
>>>
>
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