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 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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