Hi Doug and Martin,
Thanks both for your responses. I am working with PK11195, AV-1451, and PiB. In general, the standard bbregister routine with init-fsl works well for AV-1451 (adjustments needed in 30% of cases) and PiB (best performance), but it completely failed with the PK data which was acquired on the same scanner. I tried running the registration using the mean image (mri_concat --mean) but it did not help too.
All that being said, mri_coreg works extremely well for the PK11195 (only 3 manual adjustments needed so far for > 50 scans), so I am very grateful for this tool :)
If I want to run the analyses of the various PET data in the same study, will it be of concern that I am using a mix of boundary-based (AV and PIB) and normalised mutual information (PK)?
Best Wishes, Elijah
Re: [Freesurfer] mri_coreg ! http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+mri_coreg+%5C%21%22&o=newest
Martin Reuter http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Martin+Reuter%22 Mon, 16 May 2016 13:23:13 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160516
Hi,
just wanted to mention that the --cost NMI (normalized mutual information) and MI implementations in mri_robust_register are the same as spm_coreg and now mri_coreg (if the -nosym flag is specified in robust register, else it is registering in a symmetric midspace instead into the target space). If you have cases where robust_register fails, but the other tools work, let me know, because that could indicate a bug in my code.
Thanks, Martin
On 05/16/2016 03:19 PM, Douglas N Greve wrote:
It is my implementation of the spm_coreg program written by John Ashburner using normalized mutual information. I liked the spm program so much that I put the effort into replicating its behavior in C. My guess is that BBR was failing because the initialization was failing. Still I like mri_coreg for PET data because the blurriness can throw BBR off a bit. What kind of PET data do you have?
On 05/16/2016 03:06 PM, Elijah Mak wrote:
Hi Doug,
I just want to say that mri_coreg worked tremendously well for the registration of some very blurry PET-PK data. I was not getting any success with bbregister and init-fsl or mri_robust_register options.
How does this technique differ from the boundary-based registration?
Thanks a lot.
Best Wishes, Elijah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yea, I've had mixed success with PBR, Tau, and PiB. If you want to, you can tar up the anatomical and PET on the ones that fail and drop them to me here:
https://gate.nmr.mgh.harvard.edu/filedrop2
doug
On 05/16/2016 06:22 PM, Elijah Mak wrote:
Hi Doug and Martin,
Thanks both for your responses. I am working with PK11195, AV-1451, and PiB. In general, the standard bbregister routine with init-fsl works well for AV-1451 (adjustments needed in 30% of cases) and PiB (best performance), but it completely failed with the PK data which was acquired on the same scanner. I tried running the registration using the mean image (mri_concat --mean) but it did not help too. All that being said, mri_coreg works extremely well for the PK11195 (only 3 manual adjustments needed so far for > 50 scans), so I am very grateful for this tool :) If I want to run the analyses of the various PET data in the same study, will it be of concern that I am using a mix of boundary-based (AV and PIB) and normalised mutual information (PK)? Best Wishes, Elijah
Re: [Freesurfer] mri_coreg ! http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+mri_coreg+%5C%21%22&o=newest
Martin Reuter http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Martin+Reuter%22 Mon, 16 May 2016 13:23:13 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160516
Hi, just wanted to mention that the --cost NMI (normalized mutual information) and MI implementations in mri_robust_register are the same as spm_coreg and now mri_coreg (if the -nosym flag is specified in robust register, else it is registering in a symmetric midspace instead into the target space). If you have cases where robust_register fails, but the other tools work, let me know, because that could indicate a bug in my code. Thanks, Martin On 05/16/2016 03:19 PM, Douglas N Greve wrote: > It is my implementation of the spm_coreg program written by John > Ashburner using normalized mutual information. I liked the spm program > so much that I put the effort into replicating its behavior in C. My > guess is that BBR was failing because the initialization was failing. > Still I like mri_coreg for PET data because the blurriness can throw BBR > off a bit. What kind of PET data do you have? > > > On 05/16/2016 03:06 PM, Elijah Mak wrote: >> Hi Doug, >> >> I just want to say that mri_coreg worked tremendously well for the >> registration of some very blurry PET-PK data. I was not getting any >> success with bbregister and init-fsl or mri_robust_register options. >> >> How does this technique differ from the boundary-based registration? >> >> Thanks a lot. >> >> Best Wishes, >> Elijah >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu http://reuter.mit.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.
--
Elijah Mak, Gates Scholar
PhD Candidate *|* Psychiatry
University of Cambridge
Trinity College, Cambridge, CB2 1TQ
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