I'm a little puzzled by the input and reference images being the same in the first call. Assuming that this is a typo, then I cannot see why your second command would not work. Is your phase image the same size (FOV and resolution) as the magnitude images? Are you sure that the output images are blank, or could it just be that the display range is not appropriate (sometimes a bad default gets incorrectly set within the nifti image). Another thing you could try is to use "-datatype float" to force the output type (just in case it is somehow writing out truncated integers, though I would not expect this to happen).

If none of these help then you can try a sanity check by omitting the -init option (and following mat file) and using the input image as the reference as well, and then see what happens. Do let us know how you get on.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jakob Bindl <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, 15 June 2016 at 09:37
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] flirting 2d phase images

Hello,

I have a set of phase images (a time-series of one single slice) which I

want to register. So I flirted the corresponding magnitude images to the

reference image (which is the first image of the time series) and

applied the same transformation to the phase images. While the

transformation works nicely for the magnitude images, applying the same

matrices to the phase creates blank images

I did the following:

/usr/local/fsl/bin/flirt -in ../magnitude.nii -ref ../magnitude.nii -out

../reference_magnitude.nii -omat ../new_magnitude.mat -bins 256 -cost

corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -2D -dof 12

-interp trilinear

/usr/local/fsl/bin/flirt -in ../phase.nii -ref

../reference_magnitude.nii -out ../new_magnitude_shadowreg_phase

-applyxfm -init /mnt/hgfs/FSLshared/new_magnitude.mat -interp trilinear

Help would be much appreciated.

Best regards

Jakob

Dipl. Phys. Jakob Bindl

Universität Bonn

Helmholtz-Institut für Strahlen- und Kernphysik

Arbeitsgruppe Maier/Urbach

Raum 0.011

Nussallee 14-16

D-53115 Bonn

Tel: +49 (0) 228 73 3893

Fax: +49 (0) 228 73 2505

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