Dear all,
I am trying to coregister a set of PET images to a structural T1 template. The orientation of all images seems correct (ie. same labels and orientation as the standard template of fsl). I have tried the followings, but I am still not able to coregister all the images to the template:
- Bet (with and without the -R option) both the T1 and the PET images and perform flirt (default options) --> most images are coregistered but some of them are completely off target or appear squashed and with funny displays
- Bet both the T1 and PET and carry out flirt with the -2D option (carry out a rigid only), then apply flirt on the resulting rigidly transformed images (12 affine) --> the images seem to be brought closer to the target after the flirt -2D (although not overlapping), but the final coregistrations do not work and in most cases the PET images are cut and only a small piece of the image is aligned to the T1 (?)
Am I missing something? What else can I try?
Thank you very much in advance,
Best regards,
Bianca
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