Hi Birgit and Esteban,
I am applying topup only on 2 B0 images with opposite phase encoding.
The --fout option gives me the shiftmap that is then scaled with the
readout time:
topup --imain=$B0_APPA --datain=$ACPAR --config=$CONFIG --out=$TOPUP
--fout=$TOPUP_FIELD --iout=$B0_UNWARPED
fslmaths $TOPUP_FIELD -mul $READOUTTIME $SHIFT_MAP
Later, the shiftmap is converted to a deformation field (using
convertwarp) that is the applied using applywarp.
Hope that helps.
Cheers, Jan
On 06/17/2014 03:26 PM, Oscar Esteban wrote:
> Dear all,
>
> I'm also interested on getting the displacements field from topup as
> Birit. I'd really appreciate some light on this.
>
> Thanks in advance.
>
> Best,
> Oscar Esteban
>
> *______________________________________*
> *Oscar Esteban*
> PhD Student / Researcher
>
> Biomedical Image Technologies (BIT), UPM
> ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid
> (Spain)
> +34 915 495 700 ext.4234
>
> Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
> ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland
>
>
> On 28 April 2014 11:10, Birgit P <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear FSL experts,
>
>
> I have rs fMRI data which I have corrected for distortions with
> topup and applytopup. However, I would like to do my analyses on the
> distorted fMRI images and then later tranform the results to the
> 'undistorted' space. Therefore I would like to ask:
> 1. Is it possible to transform my initial regions of interest from
> the corrected fMRI space to the original distorted fMRI volumes?
> 2. Is it possible to transform the maps resulting from the fMRI
> analyses back from the original distorted fMRI volumes into the
> topup-corrected space?
>
>
> Kind regards,
> Birgit
>
>
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