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
----- 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
> These commands look just fine.
> You may want to see if the resulting fieldmap_rads is noisy at the edge
> the brain and mask it with a tighter mask (one produced by BET) to get
> rid of any noisy voxels there.
> You want the phase range to be 2*pi. It doesn't matter if it is 0 to
> or -pi to pi.
> 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,
> 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,
> 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,
>> Stamatios N Sotiropoulos
>> Clinical Neurology
>> University of Nottingham, UK