[Freesurfer] Venous system on 3D models

[rwlod...@uic.edu]

Hello my names Rich. I am working on a project that involves creating 3D
models of patient brains and placing ECoG (Electrocorticography) leads on
these models. I have intra-operative pictures of the leads placed on the
subjects and I'm using these pictures to attempt to accurately place the
leads. However, as you might guess, the 3D models are very different from
looking at a live brain and the true sulcal and gyral pattern is difficult
to determine from the pictures. I was wondering if it is possible to have
freesurfer create or mark, in some way, the veins on the models so that I
can use the venous system as points of reference when placing the leads.
If not, is there a better way to do so that you can think of? I am
relatively new to freesurfer so I don't fully understand its capability
yet. Thanks!!

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Re: [Freesurfer] Venous system on 3D models

[Zachary Greenberg]

Hi Rich,

Do you have a post-operative CT scan of your ECoG patient? If you have that
and a high-res T1, you can get very accurate reconstruction of electrode
positions on the brain surface by corregistering the two.

-zack

On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu  wrote:

> Hello my names Rich. I am working on a project that involves creating 3D
> models of patient brains and placing ECoG (Electrocorticography) leads on
> these models. I have intra-operative pictures of the leads placed on the
> subjects and I'm using these pictures to attempt to accurately place the
> leads. However, as you might guess, the 3D models are very different from
> looking at a live brain and the true sulcal and gyral pattern is difficult
> to determine from the pictures. I was wondering if it is possible to have
> freesurfer create or mark, in some way, the veins on the models so that I
> can use the venous system as points of reference when placing the leads.
> If not, is there a better way to do so that you can think of? I am
> relatively new to freesurfer so I don't fully understand its capability
> yet. Thanks!!
>
> ___
> 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.
>
>


-- 
*Zachary Greenberg*
*Assistant Imaging Specialist*
*Department of Neurological Surgery*
*University of California, San Francisco*
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Venous system on 3D models

[rwlod...@uic.edu]

I have some post-op CT's for some of my patients but not all, do you have
a link or could you explain how to coregister so I can do it for the ones
I have? Thank you!

On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
> Hi Rich,
>
> Do you have a post-operative CT scan of your ECoG patient? If you have
> that
> and a high-res T1, you can get very accurate reconstruction of electrode
> positions on the brain surface by corregistering the two.
>
> -zack
>
> On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu 
> wrote:
>
>> Hello my names Rich. I am working on a project that involves creating 3D
>> models of patient brains and placing ECoG (Electrocorticography) leads
>> on
>> these models. I have intra-operative pictures of the leads placed on the
>> subjects and I'm using these pictures to attempt to accurately place the
>> leads. However, as you might guess, the 3D models are very different
>> from
>> looking at a live brain and the true sulcal and gyral pattern is
>> difficult
>> to determine from the pictures. I was wondering if it is possible to
>> have
>> freesurfer create or mark, in some way, the veins on the models so that
>> I
>> can use the venous system as points of reference when placing the leads.
>> If not, is there a better way to do so that you can think of? I am
>> relatively new to freesurfer so I don't fully understand its capability
>> yet. Thanks!!
>>
>> ___
>> 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.
>>
>>
>
>
> --
> *Zachary Greenberg*
> *Assistant Imaging Specialist*
> *Department of Neurological Surgery*
> *University of California, San Francisco*
> ___
> 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.
>


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Re: [Freesurfer] Venous system on 3D models

[Zachary Greenberg]

Rich,

You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and
freesurfer.

First run recon-all on the patients T1 (after acpc aligning in Spm). Then
take the resultant orig.mgz file (convert to .nii using mri_convert
orig.mgz orig.nii), and corregister the post-op CT to it using SPM's
normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm
at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister
(est. and write) from the top left of the spm gui. Then chose the Orig.nii
as the reference image, and the patients pos-op CT as the target.

Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in
freeview. Click on each electrode in the CT, and copy the xyz coords from
the bottom left into a text file or matlab matrix (it will list the surface
RAS coords in bottem left of freeview, which is what you want to display on
the freesurfer pial surface).

Let me know when you get that far and I'll send you a link to some code
that will help you visualize the pial surface with overlaid electrodes.

-zack

On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu  wrote:

> I have some post-op CT's for some of my patients but not all, do you have
> a link or could you explain how to coregister so I can do it for the ones
> I have? Thank you!
>
> On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
> > Hi Rich,
> >
> > Do you have a post-operative CT scan of your ECoG patient? If you have
> > that
> > and a high-res T1, you can get very accurate reconstruction of electrode
> > positions on the brain surface by corregistering the two.
> >
> > -zack
> >
> > On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu 
> > wrote:
> >
> >> Hello my names Rich. I am working on a project that involves creating 3D
> >> models of patient brains and placing ECoG (Electrocorticography) leads
> >> on
> >> these models. I have intra-operative pictures of the leads placed on the
> >> subjects and I'm using these pictures to attempt to accurately place the
> >> leads. However, as you might guess, the 3D models are very different
> >> from
> >> looking at a live brain and the true sulcal and gyral pattern is
> >> difficult
> >> to determine from the pictures. I was wondering if it is possible to
> >> have
> >> freesurfer create or mark, in some way, the veins on the models so that
> >> I
> >> can use the venous system as points of reference when placing the leads.
> >> If not, is there a better way to do so that you can think of? I am
> >> relatively new to freesurfer so I don't fully understand its capability
> >> yet. Thanks!!
> >>
> >> ___
> >> 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.
> >>
> >>
> >
> >
> > --
> > *Zachary Greenberg*
> > *Assistant Imaging Specialist*
> > *Department of Neurological Surgery*
> > *University of California, San Francisco*
> > ___
> > 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


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.

Re: [Freesurfer] Venous system on 3D models

[rwlod...@uic.edu]

Thank you so much! This will take me some time, but i'll get back to you
when I get that far.

On Wed, October 29, 2014 9:47 pm, Zachary Greenberg wrote:
> Rich,
>
> You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab,
> and
> freesurfer.
>
> First run recon-all on the patients T1 (after acpc aligning in Spm). Then
> take the resultant orig.mgz file (convert to .nii using mri_convert
> orig.mgz orig.nii), and corregister the post-op CT to it using SPM's
> normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm
> at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister
> (est. and write) from the top left of the spm gui. Then chose the Orig.nii
> as the reference image, and the patients pos-op CT as the target.
>
> Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in
> freeview. Click on each electrode in the CT, and copy the xyz coords from
> the bottom left into a text file or matlab matrix (it will list the
> surface
> RAS coords in bottem left of freeview, which is what you want to display
> on
> the freesurfer pial surface).
>
> Let me know when you get that far and I'll send you a link to some code
> that will help you visualize the pial surface with overlaid electrodes.
>
> -zack
>
> On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu 
> wrote:
>
>> I have some post-op CT's for some of my patients but not all, do you
>> have
>> a link or could you explain how to coregister so I can do it for the
>> ones
>> I have? Thank you!
>>
>> On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
>> > Hi Rich,
>> >
>> > Do you have a post-operative CT scan of your ECoG patient? If you have
>> > that
>> > and a high-res T1, you can get very accurate reconstruction of
>> electrode
>> > positions on the brain surface by corregistering the two.
>> >
>> > -zack
>> >
>> > On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu 
>> > wrote:
>> >
>> >> Hello my names Rich. I am working on a project that involves creating
>> 3D
>> >> models of patient brains and placing ECoG (Electrocorticography)
>> leads
>> >> on
>> >> these models. I have intra-operative pictures of the leads placed on
>> the
>> >> subjects and I'm using these pictures to attempt to accurately place
>> the
>> >> leads. However, as you might guess, the 3D models are very different
>> >> from
>> >> looking at a live brain and the true sulcal and gyral pattern is
>> >> difficult
>> >> to determine from the pictures. I was wondering if it is possible to
>> >> have
>> >> freesurfer create or mark, in some way, the veins on the models so
>> that
>> >> I
>> >> can use the venous system as points of reference when placing the
>> leads.
>> >> If not, is there a better way to do so that you can think of? I am
>> >> relatively new to freesurfer so I don't fully understand its
>> capability
>> >> yet. Thanks!!
>> >>
>> >> ___
>> >> 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.
>> >>
>> >>
>> >
>> >
>> > --
>> > *Zachary Greenberg*
>> > *Assistant Imaging Specialist*
>> > *Department of Neurological Surgery*
>> > *University of California, San Francisco*
>> > ___
>> > 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
>
>
> 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 informat

Re: [Freesurfer] Venous system on 3D models

[Douglas Greve]

You can also use bbregister to register the CT to the anatomical. I'm 
not sure what steps beyond that you'd need to do.

doug

On 10/29/14 10:47 PM, Zachary Greenberg wrote:

Rich,

You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for 
matlab, and freesurfer.


First run recon-all on the patients T1 (after acpc aligning in Spm). 
Then take the resultant orig.mgz file (convert to .nii using 
mri_convert orig.mgz orig.nii), and corregister the post-op CT to it 
using SPM's normalized mutual info. routine. To do this: 1.) open 
matlab, 2.)type spm at the prompt, 3.) chose fMRI from the gui pop up, 
4.) pick corregister (est. and write) from the top left of the spm 
gui. Then chose the Orig.nii as the reference image, and the patients 
pos-op CT as the target.


Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in 
freeview. Click on each electrode in the CT, and copy the xyz coords 
from the bottom left into a text file or matlab matrix (it will list 
the surface RAS coords in bottem left of freeview, which is what you 
want to display on the freesurfer pial surface).


Let me know when you get that far and I'll send you a link to some 
code that will help you visualize the pial surface with overlaid 
electrodes.


-zack

On Wed, Oct 29, 2014 at 7:28 PM, rwlod...@uic.edu 
 mailto:rwlod...@uic.edu>> 
wrote:


I have some post-op CT's for some of my patients but not all, do
you have
a link or could you explain how to coregister so I can do it for
the ones
I have? Thank you!

On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
> Hi Rich,
>
> Do you have a post-operative CT scan of your ECoG patient? If
you have
> that
> and a high-res T1, you can get very accurate reconstruction of
electrode
> positions on the brain surface by corregistering the two.
>
> -zack
>
> On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu
 mailto:rwlod...@uic.edu>>
> wrote:
>
>> Hello my names Rich. I am working on a project that involves
creating 3D
>> models of patient brains and placing ECoG
(Electrocorticography) leads
>> on
>> these models. I have intra-operative pictures of the leads
placed on the
>> subjects and I'm using these pictures to attempt to accurately
place the
>> leads. However, as you might guess, the 3D models are very
different
>> from
>> looking at a live brain and the true sulcal and gyral pattern is
>> difficult
>> to determine from the pictures. I was wondering if it is
possible to
>> have
>> freesurfer create or mark, in some way, the veins on the models
so that
>> I
>> can use the venous system as points of reference when placing
the leads.
>> If not, is there a better way to do so that you can think of? I am
>> relatively new to freesurfer so I don't fully understand its
capability
>> yet. Thanks!!
>>
>> ___
>> 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.
>>
>>
>
>
> --
> *Zachary Greenberg*
> *Assistant Imaging Specialist*
> *Department of Neurological Surgery*
> *University of California, San Francisco*
> ___
> 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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer