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 mzamro2@illinois.edu mailto:mzamro2@illinois.edu
Begin forwarded message:
*From: *"Zamroziewicz, Marta Karolina" <mzamro2@illinois.edu mailto:mzamro2@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:
- 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.
Thanks 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
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