Re: [Freesurfer] skull strip T2 image in 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

                        >
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