I have run a bunch of cases through bbregister and overall it worked great! 315 out of about 325 cases the alignments were very good, but on 10 subjects it did very poorly. I can not so far find anything unusual about this data. Per earlier posts, I have tried the different initilization options with no luck. I also tried an fsl_rigid_register 6 DOF to create a starting .dat ,but that was way off too, maybe because it uses similar initilization information? I also saw the post to use --init-reg-out to save the init transform but I am not sure what to make of the output.
This is aligning data that has been through the 1000FC pre-processing. This converts our RAS scans to RPI, and also de-obliques using AFNI. Would you suspect either of these steps as confusing bbregister? We are using dcm2nii (mricron) for dicom to nifti conversion.
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