Hi Bruce and Douglas, After I ran through the FS, I ran the following two commands:
bbregister --s T1_0145 --mov T2_0145_file1.nii --reg register.dat --init-fsl --t2 --o outvol mri_vol2vol --mov T1_0145/mri/brain.mgz --reg register.dat --o T1_mappedToT2.nii T1_0145 is the directory for analyzing my T1 image with freesurfer, T2_0145_file1.nii is my T2 image. The result is not good. I am not sure whether there is some problem with my above two commands. Do you have any suggestion? Thanks a lot. Best, Xiaoying 2011/5/23 Xiaoying Tang <xta...@jhu.edu> > 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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