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!!
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, rwlodar2@uic.edu rwlodar2@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.
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, rwlodar2@uic.edu rwlodar2@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.
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, rwlodar2@uic.edu rwlodar2@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, rwlodar2@uic.edu rwlodar2@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
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, rwlodar2@uic.edu rwlodar2@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, rwlodar2@uic.edu rwlodar2@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.
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, rwlodar2@uic.edu mailto:rwlodar2@uic.edu <rwlodar2@uic.edu mailto:rwlodar2@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, rwlodar2@uic.edu <mailto:rwlodar2@uic.edu> <rwlodar2@uic.edu <mailto:rwlodar2@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 <mailto: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 <mailto: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 <mailto: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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
rwlodar2＠uic.edu -
Zachary Greenberg