yes, bbregister uses the surfaces generated by recon-all, so run it through to the end, then use bbregister.
cheers Bruce On Sun, 22 May 2011, Xiaoying Tang wrote: > Hi Douglas, > > Thanks for your reply! > > bbregister succeeded in running now. But I still have another question. > > You mentioned that "If you have a T1 that you've run through FS".What do you > mean by "run through"? I just ran autorecon1 to get the skullstripped T1. Do > you mean that I also have to run autorecon2 and autorecon3 if I want to use > bbregister? > > Best, > Xiaoying > > 2011/5/22 Douglas Greve <gr...@nmr.mgh.harvard.edu> > >> Do you still have version 4.1 in your path? It looks like it is calling an >> old version of fslregister. >> doug >> >> >> On 5/22/11 1:26 AM, Xiaoying Tang wrote: >> >> Hi Douglas and Bruce, >> >> I have updated my freesurfer version to 5.0.0. But I still have error when >> I tried to run bbregister. The error information is as follows" >> >> My command: bbregister --s bert --mov T2_0145_file1.nii --reg register.dat >> --init-fsl --t2 --o outvol >> >> Error information: >> >> FREESURFER_HOME >> /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0 >> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii >> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii >> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ >> reading from T2_0145_file1.nii... >> TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.999276, 0, 0.0380414) >> j_ras = (-0.00161026, 0.999104, -0.0422986) >> k_ras = (0.0380073, 0.0423292, 0.998381) >> writing to ./tmp.bbregister.16142/template.nii... >> fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg >> ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov >> --tmp ./tmp.bbregister.16142/fslregister --dof 6 >> *ERROR: Flag --niters unrecognized.* >> >> I am not sure about the reason since the Flag --niters seems to be created >> during the process, but not in my original command. >> >> I would be most grateful if you could help me solve this problem. >> >> Thanks in advance. >> >> Best, >> Xiaoying >> >> >> 2011/5/22 Xiaoying Tang <xta...@jhu.edu> >> >>> The full name on my machine is: freesurfer-centos4_x86_64-v4.1.0 >>> >>> So I think the version is 4.1.0 >>> >>> Best, >>> Xiaoying >>> >>> 2011/5/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> >>>> No, it's not the same what version are you running? >>>> >>>> >>>> >>>> On May 21, 2011, at 11:26 PM, Xiaoying Tang <xta...@jhu.edu> wrote: >>>> >>>> Hi Douglas, >>>> >>>> Thanks a lot for your suggestion. >>>> >>>> It is really strange that I don't find bbregister in the file foler of >>>> the freesurfer on my machine. But I find a program named "fslregister". Is >>>> that the same? >>>> >>>> If they are different, is it that I need to update my version of >>>> freesurfer so that I can have the program bbregister? >>>> >>>> Thanks a lot. >>>> >>>> Best, >>>> Xiaoying >>>> >>>> 2011/5/21 Douglas Greve <gr...@nmr.mgh.harvard.edu> >>>> >>>>> If you have a T1 that you've run through FS and are happy with the skull >>>>> strip, then you can register your T2 with the FS anatomical (with >>>>> bbregister), then map the skull stripped T1 into the T2 space >>>>> (mri_vol2vol), then apply it to the T2 (mri_mask). >>>>> >>>>> doug >>>>> >>>>> On 5/21/11 7:27 PM, Bruce Fischl wrote: >>>>>> Hi Xiaoying, >>>>>> >>>>>> unfortunately there isn't. I would recommend BET (from the FSL). >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Sat, 21 May 2011, >>>>>> Xiaoying Tang wrote: >>>>>> >>>>>>> Hi All, >>>>>>> >>>>>>> I am wondering whether there is any way to skull strip a T2 image >>>>> using >>>>>>> freesurfer. I tried to use the same way as for skullstripping T1 >>>>> image, but >>>>>>> always failed. >>>>>>> >>>>>>> I would be most grateful if someone can give me some suggestion. >>>>>>> >>>>>>> Best, >>>>>>> Xiaoying Tang >>>>>>> >>>>> > _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> 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
