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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