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 -- 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 _______________________________________________ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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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