Hi Dianne,
> For post-bedpost registration of standard to structural images, is it
> important that the images are in the same orientation?
> (or just that fsl accurately understands the orientation of each image)
If I understand you correctly, this is related to whether flirt
accounts for the nifti orientation. So, if you have data with
different voxel-wise orientation (e.g. sagittal vs axial
acquisitions), but for which fslview correctly labels the anatomical
axes (L-R, P-A, I-S), will flirt realise how the data are aligned?
The answer, with the current version, is no, though Mark J has posted
a script that generates a suitable initial flirt matrix:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=FSL&P=R20004
Hope that helps,
Ged
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