Dear FSL-Experts,
I am experiencing problems with Registration in FEAT. I set up my First-Level-Analyse in the FEAT GUI and tried to do Registration with the Field Maps. I did BET with the Fielmap_mag and used the following options for creating the final Field Map Magnitude: fsl_prepare_fieldmap <SIEMENS> <phase_image> <magnitude_image> <out_image> <2.46>
The B0 unwarping I have done with the prepared Field Map and the BETed Fielmap Magnitude Image.
This and the other options in the FEAT GUI seem right to me an cannot explain why the Registration is just not working.
Firstly, there is mentioned an error in the Log of FEAT:
/usr/local/fsl/bin/slicer ../example_func2highres ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres1.png ; /usr/local/fsl/bin/slicer ../highres ../example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres2.png ; /usr/local/fsl/bin/pngappend ../example_func2highres1.png - ../example_func2highres2.png ../example_func2highres.png; /bin/rm -f sl?.png ../example_func2highres2.png
Images aren't the same size!
Cannot open sla.png for reading
Images aren't the same size!
Cannot open sla.png for reading
Cannot open ../example_func2highres1.png for reading
I searched for that error and found that the problem might be that the Fieldmaps aren't the same size. But how can I fix this? I am asking myself how the Fieldmap and Fieldmap magnitude can be the same size when they are prepared totally different with fsl?
Secondly, the Registration looks just really bad. In the summary of registration it seems that the registration worked only for half of the brain. And the other half is black. Please see attached the output images (https://we.tl/J3NwIHAwry).
Any help is greatly appreciated! I am happy for every hint!
Cheers,
Eva
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