Hi Marta, I thought I was going to be ready to release it today, but my checks failed on the new script, so now I have to dig into it to see what is wrong. Check back next week. doug
On 08/01/2014 09:19 AM, Zamroziewicz, Marta Karolina wrote: > Good morning, > > I’m just checking back in about a bbregister problem that I posted > about earlier this week (see email below). I was told to check back at > the end of the week about a patch. > > Thanks so much 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> > > > Begin forwarded message: > >> *From: *"Zamroziewicz, Marta Karolina" <mzam...@illinois.edu >> <mailto:mzam...@illinois.edu>> >> *Subject: * *[Freesurfer] FLAIR Registration Problems* >> *Date: *July 29, 2014 at 1:57:58 PM CDT >> *To: *"freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> *Reply-To: * Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> >> 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> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > _______________________________________________ > 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
