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
_______________________________________________
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.
