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
