Hi,

I'm a relatively new FS user. Ive a single subject functional dataset analyzed in FSL. I ran recon-all autorecon1 ,2 and 3 on the subject's SPGR. Everything worked fine. i ran reg-feat2anat to register my functionals to the anatomical but when i hit compare button in tkregister2 , the alignment is all wrong. I tried changing the dof to 12 and maxangle to 180 but the output again looks the same. the functionals are almost inverted compared to the outline of the anatomical. During the processing i saw a warning saying that the 'neither sform or qform in the nifti-1 are valid 'and another warning saying the ' your volume will probably be incorrectly oriented'. which is evident in the output. I thought FSL and FS both use FLIRT for registration. so why are the results different? Please advise.

Regards,

Vishwadeep A. Grad. Student Medical Physics PhD Program VCU