Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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.
There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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
sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all.I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net
<test.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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
Do you mean the threshold? min=2.0 max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in that the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all.I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net
<test.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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
can you resend the image? You don't have the "invert" button clicked, do you?
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0 Thanks!
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem? _________________________________________________________________________
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in th
at
the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. _________________________________________________________________________
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. _________________________________________________________________________
【小孔成像】http://www.conxz.net
<test.jpg>
_______________________________________________ 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... 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 image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button.
I think the image is likely just a mirror image, but I failed to find a "invert" button. Where is the "invert" button?
Best!
Xiangzhen
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the "invert" button clicked, do you?
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in th
at
the lh and rh have the same number of vertices. All I can think of is to download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all.I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net
<test.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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
Hi Xiangzhen, that is something I have never seen before. I don't think it is a problem with freesurfer, and there is no button that will fix it. I think it must be something in your environment. What are the details of your platform? doug
On 06/28/2013 10:18 AM, Xiangzhen Kong wrote:
The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a "invert" button. Where is the "invert" button? Best! Xiangzhen
【小孔成像】http://www.conxz.net *From:* Bruce Fischl mailto:fischl@nmr.mgh.harvard.edu *Date:* 2013-06-28 21:56 *To:* Xiangzhen Kong mailto:bnucon@gmail.com *CC:* freesurfer mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the "invert" button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat
unique in th
at
the lh and rh have the same number of vertices. All I can think of
is to
download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com
wrote:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
【小孔成像】http://www.conxz.net
<test.jpg>
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it's on the configure overlay window, but it wouldn't cause what you are showing. I didn't notice this before but your entire color scale bar (including the text!) is mirror imaged. This is very strange, and probably explains why it looks like an rh. Can you give us the details of your environment. I don't have a clue what would cause this. Does the tkmedit window look correct? Freeview? Make sure that the text is not mirror-imaged as in this figure you sent
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button. I think the image is likely just a mirror image, but I failed to find a "invert" button. Where is the "invert" button? Best! Xiangzhen
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the "invert" button clicked, do you? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0 Thanks! _________________________________________________________________________
【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote: > Thanks very much. > Another problem, do you know why the color bar is inversed in my first > email? > Might it be related to the right-left weird problem? > > > _______________________________________________________________________
__
___ > 【小孔成像】http://www.conxz.net > > From: Bruce Fischl > Date: 2013-06-28 11:18 > To: Xiangzhen Kong > CC: freesurfer > Subject: Re: [Freesurfer] tksurfer display problem > There is no config that would do that. Fsaverage is somewhat unique in
?? ?th
at > the lh and rh have the same number of vertices. All I can think of is t
o
> download it again and see if that fixes your problem > Bruce > > > > On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote
:
> > > Actually when I just use "tksurfer fsaverage lh inflated", there is > the similar problem. > And fsaverage was copied from freesufer by recon-all. > So I think there might be something wrong with using tksurfer, e.g., > config. > > > _______________________________________________________________________
__
___ > 【小孔成像】http://www.conxz.net > > From: Bruce Fischl > Date: 2013-06-28 10:28 > To: Xiangzhen Kong > CC: freesurfer > Subject: Re: [Freesurfer] tksurfer display problem > Are you sure you didn't accidentally copy the rh over lh > > > > On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com > wrote: > > Hi all. > I want to display a result with tksurfer. The cmd is here: > tksurfer fsaverage lh inflated -overlay > ./fwhm10lh/c1.contrast/sig.mgh > That is, I want to display the result of the left hemi. > However, to my surprise, the plot seems like on the right hemi > of the brain. > In addition, the color bar is also strange. > The plot is attached. > I wonder whether this is normal or something may be wrong. > > > > > _______________________________________________________________________
__
___ > 【小孔成像】http://www.conxz.net > > <test.jpg> > > _______________________________________________ > 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... > 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 system is CentOS release 6.3. And the package of freesufer is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. I wonder whether the version mismatch(centos4 vs.centos6) causes this strange problem. I think I have to check this. (As I remember, tksurfer of this version works well in centos5.7)
PS: tkmedit works well with volumetric data. And freeview also works well.
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 22:29 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem it's on the configure overlay window, but it wouldn't cause what you are showing. I didn't notice this before but your entire color scale bar (including the text!) is mirror imaged. This is very strange, and probably explains why it looks like an rh. Can you give us the details of your environment. I don't have a clue what would cause this. Does the tkmedit window look correct? Freeview? Make sure that the text is not mirror-imaged as in this figure you sent
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button.
I think the image is likely just a mirror image, but I failed to find a "invert" button. Where is the "invert" button?
Best!
Xiangzhen
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the "invert" button clicked, do you?
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much. Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
__
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem There is no config that would do that. Fsaverage is somewhat unique in
?? ?th
at
the lh and rh have the same number of vertices. All I can think of is t
o
download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" bnucon@gmail.com wrote
:
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
__
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all.I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
__
【小孔成像】http://www.conxz.net
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Hi, Bruce and Douglas. Thanks for your patient reply. I have checked the problem with the latest freesurfer, but the problem is still there. Now I am sure that what I get with the tksurfer is a up-down mirror image (see the attached). If the image is put upside down, it will be ok. As I know, in normal condition, the color bar is actually located at the bottom right corner.
This is a weired problem. If you would like to help me solve this problem, I will appreciated it. If not, I think I can also use it for visualization now with a subsequent flip.
Thanks very much.
Xiangzhen
On Sat, Jun 29, 2013 at 12:03 AM, Xiangzhen Kong bnucon@gmail.com wrote:
** The system is CentOS release 6.3. And the package of freesufer is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. I wonder whether the version mismatch(centos4 vs.centos6) causes this strange problem. I think I have to check this. (As I remember, tksurfer of this version works well in centos5.7)
PS: tkmedit works well with volumetric data. And freeview also works well.
【小孔成像】http://www.conxz.net
*From:* Bruce Fischl fischl@nmr.mgh.harvard.edu *Date:* 2013-06-28 22:29 *To:* Xiangzhen Kong bnucon@gmail.com *CC:* freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* Re: Re: [Freesurfer] tksurfer display problem it's on the configure overlay window, but it wouldn't cause what you are showing. I didn't notice this before but your entire color scale bar (including the text!) is mirror imaged. This is very strange, and probably explains why it looks like an rh. Can you give us the details of your environment. I don't have a clue what would cause this. Does the tkmedit
window look correct? Freeview? Make sure that the text is not mirror-imaged as in this figure you sent
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
The image is attached. The following cmd is all I did. tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh And I did not click any button.
I think the image is likely just a mirror image, but I failed to find a "invert" button. Where is the "invert" button?
Best!
Xiangzhen
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 21:56 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem can you resend the image? You don't have the "invert" button clicked, do you?
On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Do you mean the threshold? min=2.0 max=5.0
Thanks!
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 20:57 To: Xiangzhen Kong CC: freesurfer Subject: Re: Re: [Freesurfer] tksurfer display problem sorry, I didn't notice that. What were your min and max set to? On Fri, 28 Jun 2013, Xiangzhen Kong wrote:
Thanks very much.
Another problem, do you know why the color bar is inversed in my first email? Might it be related to the right-left weird problem?
__
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 11:18 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem
There is no config that would do that. Fsaverage is somewhat unique in
?? ?th
at
the lh and rh have the same number of vertices. All I can think of is t
o
download it again and see if that fixes your problem Bruce
On Jun 27, 2013, at 10:51 PM, "Xiangzhen Kong" <bnucon@gmail.com
wrote :
Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config.
__
【小孔成像】http://www.conxz.net
From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh
On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" bnucon@gmail.com wrote:
Hi all.I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong.
__
【小孔成像】http://www.conxz.net
<test.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Xiangzhen Kong