Good morning,

I wrote several weeks ago about a bbregister problem that we’ve encountered (I’ve attached the original email below). I’d like to check back in about the status of the patch that was being developed.

Thank you for your time and assistance!

Marta Zamroziewicz
MD/PhD Candidate

Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
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:

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. 

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