Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Bruce Fischl]

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



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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

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 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
>>
>>
>>
>>
>>
>
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> 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
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Bruce Fischl]

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   

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 
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






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e-mail
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HelpLine at
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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

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 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   
>
> 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 > >
>> 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.
>>
>>
>>
>>
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

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 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 
> 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   
>>
>> 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 <
>>> fis...@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.
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

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 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 
> 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 
>> 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   
>>>
>>> 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 <
 fis...@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.




>>
>
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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Bruce Fischl]

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  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  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  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   

  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 

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






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contains patient information, please contact the Partners Compliance
HelpLine at
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