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FSL  June 2008

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Subject:

Re: EPI distortion correction using FUGUE

From:

Stamatis Sotiropoulos <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 25 Jun 2008 23:33:18 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (75 lines)

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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