Hi Mark,
/usr/local/fsl/bin/flirt -in ../magnitude.nii -ref ../reference_magn.nii -out../new_magnitude.nii -omat ../new_magnitude.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -2D -dof 12 -interp trilinearworks fine, applying the resulting matrix to the same image again by
/usr/local/fsl/bin/flirt -in ../magnitude.nii -applyxfm -init../new_magnitude.mat -out ../test.nii -paddingsize 0.0 -interp trilinear -ref ../reference_magn.niialso gives me a blank image.
[log in to unmask]" type="cite">Hi,
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.
All the best,Mark
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 Iwant to register. So I flirted the corresponding magnitude images to thereference image (which is the first image of the time series) andapplied the same transformation to the phase images. While thetransformation works nicely for the magnitude images, applying the samematrices 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 -costcorratio -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 BindlUniversität BonnHelmholtz-Institut für Strahlen- und KernphysikArbeitsgruppe Maier/Urbach
Raum 0.011Nussallee 14-16D-53115 Bonn
Tel: +49 (0) 228 73 3893Fax: +49 (0) 228 73 2505E-Mail: [log in to unmask]
-- 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 E-Mail: [log in to unmask] www.mrt.uni-bonn.de