From
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/ApplytopupFurtherInformation:
N.B. least-squares resoration can only be performed on pairs of (two or
more) scans with phase-encoding along the same axis. It is e.g. not
possible to perform least-squares restoration on one image acquired with
left->right phase-encoding and another with anterior->posterior.
If one has data with left->right, right->left,
anterior->posterior and posterior->anterior encoding one can
perfrom least-squares restoration on the two pairs independently and
then average them (or enter both into fdt/bedpost independently).
---
So, sounds like you should try --method=jac
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 12/14/12 3:03 PM, "Mark Elliott" <[log in to unmask]> wrote:
>I am trying to use applytopup and get the following error:
>
>terminate called after throwing an instance of
>'TOPUP::ApplyTopupException'
> what(): ApplyTopup:: msg=Invalid combination of phase-encode vectors
>for
>least-squares restoration
>Aborted
>
>
>My commands looks like this:
>
>> cat topup_params.txt
>0 1 0 0.0508
>0 -1 0 0.0508
>
>> applytopup --imain=dti.nii --datain=topup_params.txt --inindex=1
>--topup=topup_out --out=dti_topup
>
>My data file ("dti.nii") contains 87 DWIs (some b=0, some b!=0) all
>acquired
>with the same PE scheme. I made the topup fieldmap with a 2 volume dataset
>built from the first b=0 volume of "dti.nii" and a b=0 volume acquired
>with
>reversed PE (hence the syntax of "topup_params.txt"). The topup command
>ran
>fine, and was:
>
>> topup --imain=topup_in.nii --datain=topup_params.txt --out=topup_out
>--fout=topup_fout --iout=topup_iout
>
>
>
>Any help is greatly appreciated.
>
>Mark.
>
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