what do you mean that the result is not good? Does the freesurfer analysis look ok?
Xiaoying Tang wrote: > 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 <mailto:xta...@jhu.edu>> > > I see. > > Thanks a lot. > > > Xiaoying > > 2011/5/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 <mailto: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 > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
