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

>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center

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