I see. Thanks a lot.
Xiaoying 2011/5/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > 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 >>>>> >>>>> >>>>> >>>> >>> >>
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