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