Hi all,
One of my regions of interest is the OFC, and so we have decided to angulate the slices (-45degress from x) in order to attempt to maximise the signal in this area. Is there any reason why such slice angulation of the BOLD data might impact on the registration process during FEAT?
We are including B0 unwarping with the fieldmap, and I am also using non-linear registration to standard space, but the results are not good. I have interrogated the results of the registration within Feat and it seems reasonable (I think), but when I use flirt to transform thresh_zstat1.nii.gz into standard space (by applyxfm of the examplefunc2standard.mat), I end up with blobs of activation outside of the standard brain. I use the following command:
flirt -in thresh_zstat1.nii.gz -ref reg/standard.nii.gz -applyxfm -init reg/example_func2standard.mat -interp trilinear -out thresh_zstat1_standard.nii.gz
Any ideas of how I can improve the registration here?
many thanks
Ella
|