That is the right idea, but you have to get it relatively close or it won't start in the right place. If the slab (functional or T1) were acquired in the same session, use --init-header.
doug On 12/16/10 4:40 PM, Leonardo Barbosa wrote: > I had trouble with that this week (creating a register.dat for partial > fmri). But I had a partial structural MRI acquired just after the fMRI > session. Then I tried to run > > bbregister --s subj1 --mov t1struct1.img --init-fsl --t1 --reg register.dat > > to create a initial register.dat. After that I opened it with tkregister2 > > tkregister2 --mov t1struct1.img --reg register.dat --surf > > and manually moved the partial fmri close to the "right place" over > the anatomical image. After that I saved the register.dat and used > > bbregister --s subj1 --mov t1struct1.img --init-reg register.dat --t1 > --reg register2.dat > > to create a better register2.dat. It seems to be pretty good from 1 > subject, and bad for the other. > > I couldn't find information about --init-reg in the wiki, only running > with --help "Supply an initial registration matrix." . So don't know > how it works... I'm imagining the obvious, that the algorithm of > bbregister uses the matrix in register.dat as initial point for > searching the right position. > > Best Regards > Leonardo Barbosa > www.if.usp.br > > On Wed, Dec 15, 2010 at 9:54 PM, Joakim Vinberg<jvinb...@omneuron.com> wrote: >> Hi everybody, >> >> >> >> I am working towards multi-modal integration of BOLD data. For some of my >> data, the entire brain was not recorded (in this case, I have 12 slices >> covering the superior half of the brain). I have been working to align this >> data using bbregister and have had very inconsistent results: in 1 subject >> it worked great; in another 6, the alignment failed (resulting in an >> alignment that is sometimes close, and sometimes way off). >> >> >> >> I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I have >> used this method successfully with a number of other sessions so far (with >> functional slabs that do cover the entire brain) with outstanding results. >> >> >> >> Is this troublesome for bbregister, or is there potentially something I’m >> doing incorrectly? >> >> >> >> Thanks in advance! If I’m repeating well-worn topics, I apologize, I >> couldn’t find anything following a search through the archives. >> >> >> >> Joakim >> >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
