I see.
Thanks a lot.
Xiaoying
2011/5/22 Bruce Fischl fischl@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 greve@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 xtang7@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 fischl@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 xtang7@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 greve@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 >> >> > _______________________________________________
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