Hi All,
I am now trying to do inhomogeneity correction for T1 images. I find that
there are two commands: nu_correct and mri_nu_correct.mni in Freesurfer. I
am not sure about the difference between these two commands. To me, they
seem to be the same
I would be glad if someone could answer my
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
> what do you mean that the result is not good? Does the freesurfer analysis
> look ok?
>
> Xiaoying Tang wrote:
>
>>
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
> I see.
>
> Thanks a lot.
>
>
> X
I see.
Thanks a lot.
Xiaoying
2011/5/22 Bruce Fischl
> 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,
>>
>>
n that I also have to run autorecon2 and autorecon3 if I want to use
bbregister?
Best,
Xiaoying
2011/5/22 Douglas Greve
> 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
f you could help me solve this problem.
Thanks in advance.
Best,
Xiaoying
2011/5/22 Xiaoying Tang
> 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
>
>> No,
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
> No, it's not the same what version are you running?
>
>
>
> On May 21, 2011, at 11:26 PM, Xiaoying Tang wrote:
>
> Hi Douglas,
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
> > Br
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
Okay, thanks!
Best,
Xiaoying
2011/4/25 Bruce Fischl
> yes, I think that's a typo and should be autorecon2. Perhaps Nick can
> confirm?
>
>
> On Mon, 25 Apr 2011, Xiaoying Tang wrote:
>
> Hi All,I find the following content on the wikipage of freesurfer:
>>
>
econ2
-autorecon3 -s **" since we have already run the -autorecon1
via **"recon-all
-autorecon1 -noskullstrip -s "?
Thanks a lot for your answering.
Best,
Xiaoying Tang*
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Freesurfer@nmr.m
you mean the ventricles? They are pretty big and may not have been
> labeled accurately. The cortex is hard to tell the way you have it windowed.
>
> cheers
> Bruuce
>
> On Fri, 10 Dec 2010, Xiaoying Tang wrote:
>
> Hi All,
>>
>> When use tkemedit to view
ation using freesurfer
To: Xiaoying Tang
Cc: freesurfer@nmr.mgh.harvard.edu
> not sulcal CSF (which you really can't get from just a T1), but you
> can
> measure ventricular CSF
> On Wed, 17 Mar 2010, Xiaoying Tang wrote:
>
> > Hi All,
> >
> > Is it possible
Hi All,
Is it possible to get only csf via using freesurfer to do segmentation?
Best,
Xiaoying
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is in
Hi all,
After autorecon3, there are two files named wm.mgz and wmparc.mgz. What's the
difference between this two? If I just want the white matter, should I use
wm.mgz or wmparc.mgz? The corresponding grey matter is aparc+aseg.mgz.
Looking forward to your early reply.
Best,
Xiaoying
__
Hi Allison,
You are so helpful. Thanks a lot.
Best,
Xiaoying
- Original Message -
From: Allison Stevens
Date: Friday, March 12, 2010 7:43 am
Subject: Re: [Freesurfer] problem on recon-all
To: Xiaoying Tang
Cc: freesurfer@nmr.mgh.harvard.edu
> Xiaoying,
> There are directions f
Hi all,
When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in
sequence. But now suppose I have already have a very good skull-stripped
subject. I mean I don't need to do skull-stripping with freesurfer. But I want
to get greymatter and white matter, which are generated i
Hi all,
Is there someone who can teach me how to get the separate grey matter like the
white matter(wm.seg.mgz)? I have run the commands autorecon1 autorecon2 and
autorecon3, but I still can't find the separate grey matter.
I would be most grateful if someone who can help me.
Best,
Xiaoying
__
t: Re: [Freesurfer] problem on freesurfer
To: Xiaoying Tang
Cc: ni...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu
> Hi Xiaoying,
>
> there are gray matter estimates in aseg.mgz, but you need to run
> autorecon3 to get the surfaces that let us estimate cortical gm m
Hi Nick,
Sorry, I am not sure whether I can successfully post my problem on the mailing
list. So I send you the email and cc it to the mailing list.
I now have a problem on freesurfer. After run auto-recon2, I am supposed to get
grey matter and white matter. The white matter is in the form of w
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