It is actually a change to recon-all, which you can get here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/recon-all
Run it with --bbr-init-header
doug
On 08/25/2014 10:35 AM, Zamroziewicz, Marta Karolina wrote:
Good morning!
Is the bbregister patch available yet (original email below)?
Thank you for your time and assistance!
Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2@illinois.edu mailto:mzamro2@illinois.edu 815-980-3882
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:
- 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;
- 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.
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