So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too.
Any help would be appreciated.
Katie
Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do?
sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote:
So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too.Any help would be appreciated.
Katie
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different.
Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do?
sorry, Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
So our lab is running a couple analyses and we are gettingdifferent results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated.
Katie
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/**compliancelinehttp://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.
Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try:
select_talairach_point <xtal> <ytal> <ztal>
cheers Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. KatieThe 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.
Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly?
Thanks for all your help! Katie
On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try:
select_talairach_point <xtal> <ytal> <ztal>
cheers
Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a
talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. KatieThe 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/**compliancelinehttp://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.
Nevermind, it turns out it was due to an permissions error.
Thanks again.
Katie
On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt kcb@wjh.harvard.eduwrote:
Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly?
Thanks for all your help! Katie
On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try:
select_talairach_point <xtal> <ytal> <ztal>
cheers
Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a
talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. KatieThe 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/**compliancelinehttp://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.
Another question. If I have a list of talairach coordinates, is there someway to load those without having to do it individually? Or someway to save the points after scripting to run through select_talairach_point individually (as just redoing the command will lose the previous point each time)?
Katie
On Wed, Sep 5, 2012 at 2:02 PM, Katie Bettencourt kcb@wjh.harvard.eduwrote:
Nevermind, it turns out it was due to an permissions error.
Thanks again.
Katie
On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt kcb@wjh.harvard.eduwrote:
Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly?
Thanks for all your help! Katie
On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try:
select_talairach_point <xtal> <ytal> <ztal>
cheers
Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a
talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. KatieThe 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/**compliancelinehttp://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.
Hi Katie
what do you want to do with them? Bruce
On Tue, 11 Sep 2012, Katie Bettencourt wrote:
Another question. If I have a list of talairach coordinates, is there someway to load those without having to do it individually? Or someway to save the points after scripting to run through select_talairach_point individually (as just redoing the command will lose the previous point each time)? Katie
On Wed, Sep 5, 2012 at 2:02 PM, Katie Bettencourt kcb@wjh.harvard.edu wrote: Nevermind, it turns out it was due to an permissions error. Thanks again.
Katie
On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt kcb@wjh.harvard.edu wrote: Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie
On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point <xtal> <ytal> <ztal> cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Katie Bettencourt