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
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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list 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.
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
Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailto: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 <mailto: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 <mailto: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 <mailto: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 >> > _______________________________________________ > 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
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
Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > _______________________________________________ Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 >> >> > _______________________________________________
> Freesurfer mailing list > 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
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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 xtang7@jhu.edu
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 >>> >>> > _______________________________________________ > >> Freesurfer mailing list >> 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <xtang7@jhu.edu mailto:xtang7@jhu.edu>
I see. Thanks a lot. Xiaoying 2011/5/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 > _______________________________________________ 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
Hi Douglas,
Thanks for your reply.
I think I have solved the problem -- I made a silly mistake myself.....
Best, Xiaoying
2011/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu
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 <xtang7@jhu.edu mailto:xtang7@jhu.edu>
I see.
Thanks a lot.
Xiaoying
2011/5/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 > _______________________________________________ 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
greve@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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Xiaoying Tang