Hello,
I’m trying to update recon-all (with freesurfer-6) on a number of subjects using T2 FLAIR images and the following command: recon-all -subjid <subject_name> -FLAIR <path_to_FLAIR.nii.gz> -FLAIRpial -autorecon3
For a substantial portion of subjects, the registration of the FLAIR image to the T1 fails. I’ve run a few trials where I pre-registered the FLAIR to the T1 and made sure the header information was the same (with fslcpgeom), but the registration during recon-all still fails (see images below).
I saw a few posts from a couple years back about a recon-all patch that may fix the registration issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39378.html Is this the best way to deal with this issue?
Thanks very much,
Dan
[cid:image001.jpg@01D45260.EDE8C4E0]
It is hard to tell from the images, but it looks like that flair has very little gray/white contrast. Can you send the bbregister log file? It should be something like subject/mri/transforms/FLAIRraw.auto.dat.log
On 9/22/18 1:42 PM, Albrecht, Daniel S. wrote: Hello,
I’m trying to update recon-all (with freesurfer-6) on a number of subjects using T2 FLAIR images and the following command: recon-all -subjid <subject_name> -FLAIR <path_to_FLAIR.nii.gz> -FLAIRpial -autorecon3
For a substantial portion of subjects, the registration of the FLAIR image to the T1 fails. I’ve run a few trials where I pre-registered the FLAIR to the T1 and made sure the header information was the same (with fslcpgeom), but the registration during recon-all still fails (see images below).
I saw a few posts from a couple years back about a recon-all patch that may fix the registration issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39378.html Is this the best way to deal with this issue?
Thanks very much,
Dan
[cid:part2.51ECB190.54C00CD2@mgh.harvard.edu]
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Hi Doug,
Please find the bbregister log attached here. One thing I just realized is that I was registering the FLAIR to the original T1 image (which was 0.5mm iso) and not the T1.mgz image. I ran a test where I registered the FLAIR to the T1.mgz image, but the resulting bbregister output was still off, although not as bad as previously (the image planes matched up). I also tried using –init-spm with the bbregister, but with similar results. I can send screenshots of that or raw images if it would be informative.
Thanks,
Dan
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, September 23, 2018 at 7:27 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Misregistration of T2 FLAIR during recon-all
It is hard to tell from the images, but it looks like that flair has very little gray/white contrast. Can you send the bbregister log file? It should be something like subject/mri/transforms/FLAIRraw.auto.dat.log On 9/22/18 1:42 PM, Albrecht, Daniel S. wrote: Hello,
I’m trying to update recon-all (with freesurfer-6) on a number of subjects using T2 FLAIR images and the following command: recon-all -subjid <subject_name> -FLAIR <path_to_FLAIR.nii.gz> -FLAIRpial -autorecon3
For a substantial portion of subjects, the registration of the FLAIR image to the T1 fails. I’ve run a few trials where I pre-registered the FLAIR to the T1 and made sure the header information was the same (with fslcpgeom), but the registration during recon-all still fails (see images below).
I saw a few posts from a couple years back about a recon-all patch that may fix the registration issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39378.html Is this the best way to deal with this issue?
Thanks very much,
Dan
[cid:part2.51ECB190.54C00CD2@mgh.harvard.edu]
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Albrecht, Daniel S. -
Greve, Douglas N.,Ph.D.