Hello Lilla, thanks for the answer. I first used
bbregister --s (Freesurfer Directory) --mov b0.nii --reg .dat --dti --init-fsl Afterwards I made some minor spatial changes to the aparc+aseg, bringing it closer to what i believed its position was on the b0space: tkregister2 --mov b0.img --reg .dat --surf As far as I understand the aparc+aseg was the target and the b0 the space difining image. Now again the T1 should be the target and the b0 should remain constant. You mean that even if I want to register the T1 to the b0 i have to set the b0 as target? Thanks Constantin Quoting Lilla Zollei <lzol...@nmr.mgh.harvard.edu>: > > Hi Constantin, > > When you used tkregister2 which volume was the target? Acoording to > what you write it was the b0 volume. So when you apply the registration > to the T1 volume, you should keep it that way. > > --mov T1 > --targ b0image > and no -inv is necessary. > > Let me know if I misunderstood what you were doing. > > Lilla > > On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote: > >> Hellom >> >> I coregistered manually a aparc+aseq.nii file to my DWI-space with >> tkregister2. I saved the .dat file and applied it later to the T1 >> image in order to apply the same spatial coregistration as to the >> aparc+aseg. For woth the aparc+aseg and the T1 I used the command >> mri_vol2vol >> --mov was the b0image >> --targ was the aparc+aseg and T1 respectively >> --o was the output (a .nii in both cases) >> --reg was the .dat file >> and at the and --inv. >> >> While the aparc+aseg registration to the b0 worked, the >> T1-registration gave a false result (altough it had the same >> dimensions and was in the same space with the aparc+aseg). >> >> What am I doing wrong? Is the mri_vol2vol command the wrong one? I >> want to apply the same changes as to the aparc+aseg, as they are saved >> in the .dat file. >> >> Thanks a lot, >> Constantin >> >> >> _______________________________________________ >> 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
