Hi,
Just to clarify the previous responses here:
The current version does use a single interpolation, as stated in the help text:
"If you are running both motion correction and B0 unwarping, the motion correction resampling does not get applied at the same time as the motion estimation; instead the motion correction gets applied simultaneously with the application of the B0 unwarping, in order to minimise interpolation-related image blurring."
The current version does not use spline interpolation (it uses trilinear) but that can readily be changed by adding --interp=spline to the following line of the featlib.tcl file:
fsl:exec "${FSLDIR}/bin/applywarp -i grot$pad -o grot$pad --premat=mc/prefiltered_func_data_mcf.mat/MAT_$pad -w reg/example_func2highres_warp.nii.gz -r example_func --rel --postmat=reg/highres2example_func.mat"
If you are working on a shared system and not everyone wants this change then you will need to make your own copy of the fsl tree and set your environment variables to point to that version.
All the best,
Mark
On 7 Oct 2013, at 18:50, Matt Glasser <[log in to unmask]<mailto:[log in to unmask]>>
wrote:
Unless it's been changed, I don't think it's a single interpolation. Also I don't think it's a spline interpolation.
Peace,
Matt.
From: Diederick Stoffers <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>>
Date: Monday, October 7, 2013 12:23 PM
To: <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] Apply rs-fMRI motion correction and fieldmap-based unwarping in a single interpolation
Feat will do this for you.
Cheers,
Diederick
On 7 Oct 2013, at 18:54, Torsten Rohlfing <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi All:
In our rs-fMRI data, we would like to correct both B0 field-induced distortion (using FUGUE) and motion (using mcflirt?), but in a single (!) interpolation operation.
Is it possible to perform a single reslice using the concatenation of fieldmap-based unwarping and rigid motion transformation? Would we do this using flirt, can fugue do it, or would we need to do some more involved transformation computations?
Hope this makes sense. Thanks!
Torsten
