Dear List, I've been quite frustrated with the BBRegister results when trying to register a partial field of view EPI mean functional image to a T1 scan. I've tried different init arguments (fsl, spm, header) and none really work. I've found that the initial registration is causing the problem, since the T1 and mean EPi are in reasonable alignment, but not perfect. As soon as it passes the initial alignment it's totally off and obviously fails in the BBR step. I have no full head EPI, unfortunately. I have a full head scout which seems to be a T1 image with really poor contrast. If I try to register this to the T1 through BBRegister it works. But if I use it as an intermediate file it still fails. What can I do? How does the intermediate file come into play? Will it get registered to the T1 initially and then the resulting matrix is used further? I also tried to feed the resulting registration matrix as init-reg but that didn't work either.
Is there a way to skip the initial registration? Can I mask the T1 image with the FoV of the functional scan if they are initially in reasonable alignment? Would that work? Would that mean that I have to re-run ReconAll with the masked T1? Would love to hear back from someone. Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: [email protected] _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
