Hello,
I want to make cortical surface images that we will overlay with our own masks. But we want to do this in native space. So, I was wondering if it is possible to go thorugh the reconstruction process to make the surfaces without ever using the talairach transform and keeping everything in its native space.
Thank you,
Adam
adam --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we will overlay with our own masks. But we want to do this in native space. So, I was wondering if it is possible to go thorugh the reconstruction process to make the surfaces without ever using the talairach transform and keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular phones from your PC http://us.rd.yahoo.com/mail_us/taglines/postman5/*http://us.rd.yahoo.com/evt=39666/*http://messenger.yahoo.com and save big.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
------------------------------------------------------------------------
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
adam
__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
specify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote:
Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
adam
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
specify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote: Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
------------------------------------------------------------------------
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
------------------------------------------------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote:
Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote:
I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this: tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat It is assumed that rawavg.mgz is in the native space (same This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol specify your roi volume as the --mov and use nearest neighbor interp doug adam walczak wrote:Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
adam
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
adam
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Thanks...that worked. I am also trying to create a flattened image to overlay my ROI data on. Will I need to make a new overlay with the flattened image as the surface template?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote: Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
specify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote: Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
------------------------------------------------------------------------
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
------------------------------------------------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, you should be able to overlay it on and surface configuration or patch from that hemisphere.
Bruce
On Tue, 30 May 2006, adam walczak wrote:
Thanks...that worked. I am also trying to create a flattened image to overlay my ROI data on. Will I need to make a new overlay with the flattened image as the surface template?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote: Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2volspecify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote: Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, on "any" surface configuration....
On Tue, 30 May 2006, Bruce Fischl wrote:
no, you should be able to overlay it on and surface configuration or patch from that hemisphere.
Bruce
On Tue, 30 May 2006, adam walczak wrote:
Thanks...that worked. I am also trying to create a flattened image to overlay my ROI data on. Will I need to make a new overlay with the flattened image as the surface template?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote: Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve greve@nmr.mgh.harvard.edu wrote: I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2volspecify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote: Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
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
thank you.
Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sorry, on "any" surface configuration....
On Tue, 30 May 2006, Bruce Fischl wrote:
no, you should be able to overlay it on and surface configuration or patch from that hemisphere.
Bruce
On Tue, 30 May 2006, adam walczak wrote:
Thanks...that worked. I am also trying to create a flattened image to overlay my ROI data on. Will I need to make a new overlay with the flattened image as the surface template?
Thanks.
Adam
Doug Greve wrote: You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote: Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve wrote: I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2volspecify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote: Doug,
I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that an answer to your question?
Adam
--- Doug Greve wrote:
What do you mean by "native space"? The reconstruction is not done in tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
New Yahoo! Messenger with Voice. Call regular
phones from your PC
and save big.
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
adam --------------------------------- Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.
freesurfer@nmr.mgh.harvard.edu
-
adam walczak -
Bruce Fischl -
Doug Greve