The current version of recon-all does not have any flexibility with regard to bbr. I'm developing a patch that will allow this to be fixed. Check back at the end of the week. doug
On 07/29/2014 02:57 PM, Zamroziewicz, Marta Karolina wrote: > Hello, > > This email is related to the archived “bbregister and FLAIR” email > chain posted by Kayle Sawyer on 5/23/2014 > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html). > > > We have also been registering with FLAIR scans, and have run into a > problem with approximately half of our subjects. Recon-all completes > successfully but a bad registration step leaves our MPRAGE and FLAIR > scans misaligned. I’ve attached two screenshots, the first of which > shows a bad registration and the second of which shows a good > registration. > > Per your previous suggestion, we ran bbregister using the following flag: > bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat > --t2 --lta reg.test.lta > > This did result in a good registration, and we are hoping to > incorporate this into our processing pipeline to ensure that we can > use the FLAIR for refining the pill surface. The problem that we’ve > run into is that we aren’t sure at which point this bbregister step > occurs within the recon-all process flow. We were thinking there are a > couple of possibilities: > > 1. manually create the transformation matrix for the FLAIR using the > command mentioned above, and then re-run whichever steps necessary in > recon-all to include this manually created xform; > > 2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image > to create a new, properly aligned mri/FLAIR.mgz, and then re-run > recon-all with whatever steps/flags we need to include this FLAIR > image to refine the pial surface. > > Unfortunately we're not exactly sure which flags to include in > recon-all in order to most efficiently re-process our data with the > manually created FLAIR transformation, and we were hoping you might > offer some advice on this point. Please let me know if I can provide > any additional information. > > Thanks for your time and assistance! > > > > > > > > Marta Zamroziewicz > MD/PhD Candidate > Decision Neuroscience Laboratory > University of Illinois Urbana-Champaign > mzam...@illinois.edu <mailto:mzam...@illinois.edu> > 815-980-3882 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
