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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