Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter, but when I overlay functional activations on it, it seems to be surface of white matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same talairach coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and load it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter, but when I overlay functional activations on it, it seems to be surface of white matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same talairach coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and load it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white surface? (I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter,
but
when I overlay functional activations on it, it seems to be surface of
white
matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and
load
it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
Hi George,
I'll leave this for Doug. I think the more standard stream is to use mri_vol2surf to sample your fMRI volume onto the surface. It has explicit parameters that control how you sample, but again once you've sampled it you can display it on *any* surface and it will look the same (white, pial, inflated, etc...)
cheers, Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white surface? (I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter,
but
when I overlay functional activations on it, it seems to be surface of
white
matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and
load
it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf
doug
Bruce Fischl wrote:
Hi George,
I'll leave this for Doug. I think the more standard stream is to use mri_vol2surf to sample your fMRI volume onto the surface. It has explicit parameters that control how you sample, but again once you've sampled it you can display it on *any* surface and it will look the same (white, pial, inflated, etc...)
cheers, Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white surface? (I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter,
but
when I overlay functional activations on it, it seems to be surface of
white
matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and
load
it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up? what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ? Thanks, George
On Feb 6, 2008 1:33 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf
doug
Bruce Fischl wrote:
Hi George,
I'll leave this for Doug. I think the more standard stream is to use mri_vol2surf to sample your fMRI volume onto the surface. It has explicit parameters that control how you sample, but again once you've sampled it you can display it on *any* surface and it will look the same (white, pial, inflated, etc...)
cheers, Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white surface? (I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter,
but
when I overlay functional activations on it, it seems to be surface
of
white
matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it,
and
load
it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
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
George He wrote:
Hi, suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up?
In theory, just the stuff in the middle, though usually the voxel size is so big that it gets both surfs. You can also use --interp trilinear to interpolate. You can also use --projfrac-avg to average across the ribbon.
what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ?
It will sample outside of the brain.
doug
Thanks, George
On Feb 6, 2008 1:33 PM, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf doug Bruce Fischl wrote: > Hi George, > > I'll leave this for Doug. I think the more standard stream is to use > mri_vol2surf to sample your fMRI volume onto the surface. It has > explicit parameters that control how you sample, but again once you've > sampled it you can display it on *any* surface and it will look the > same (white, pial, inflated, etc...) > > cheers, > Bruce > > > On Tue, 5 Feb 2008, George He wrote: > >> Hi Bruce, >> Thanks for your reply. The command I used to visualize is: >> tksurfer SUBJID rh inflated -overlay >> allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz >> \ >> -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ >> -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot >> what is the option to make the overlay displayed, say, on the pial >> surface, >> or on the face that is at the middle of the pial and the white surface? >> (I don't see a sampling option in tksurfer help.) >> George >> >> >> On Feb 5, 2008 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >>> Hi George, >>> >>> there are two different questions here: (1) what anatomical boundary >>> does >>> each surface represent, and (2) how do you sample functional data onto >>> the surface. For (1) the pial surface is indeed the boundary between >>> gray >>> matter and CSF, but for (2) once you choose a sampling strategy >>> (anywhere >>> from gray/white out to pial) the fMRI data can be displayed on any >>> of the >>> surfaces simply as a visualization. Is that clear? >>> >>> Bruce >>> >>> >>> On Tue, 5 Feb 2008, George He wrote: >>> >>>> Hi freesurfer experts, >>>> It seems to me the pial surface should be the surface of gray matter, >>> >>> but >>> >>>> when I overlay functional activations on it, it seems to be surface of >>> >>> white >>> >>>> matter. >>>> The reason I think so is that when I load the same activation in both >>>> tksurfer and tkmedit, >>>> if I click on an activated area (or any point) on the pial surface in >>>> tksurfer, save it, and load it in tkmedit, the point will land on the >>>> yellow/green lines while the tksurfer and tkmedit show the same >>> >>> talairach >>> >>>> coordinate for the point. >>>> If I click on a point that is on the red line in tkmedit, save it, and >>> >>> load >>> >>>> it in tksurfer, they (tkmedit and tksurfer) show different talairach >>>> coordinates for the points. >>>> Question: what is the truth and what should I expect? >>>> Thanks, >>>> George >>>> >>> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
Thanks Doug. I think I get the idea now. There is one thing that still bothers me though, which I described in my original email: suppose the same pial surface is loaded in tksurfer and tkmedit. If I click on the pial surface in tksurfer, save the point and load it in tkmedit, it always ends up on the white surface in tkmedit. Why not on the pial surface? (This has nothing to do with functional data overlay.) best, George
On Feb 6, 2008 2:07 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
George He wrote:
Hi, suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up?
In theory, just the stuff in the middle, though usually the voxel size is so big that it gets both surfs. You can also use --interp trilinear to interpolate. You can also use --projfrac-avg to average across the ribbon.
what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ?
It will sample outside of the brain.
doug
Thanks, George
On Feb 6, 2008 1:33 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf
doug
Bruce Fischl wrote:
Hi George,
I'll leave this for Doug. I think the more standard stream is to use mri_vol2surf to sample your fMRI volume onto the surface. It has explicit parameters that control how you sample, but again once you've sampled it you can display it on *any* surface and it will look the same (white, pial, inflated, etc...)
cheers, Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white
surface?
(I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data
onto
the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray
matter,
but
when I overlay functional activations on it, it seems to be surface
of
white
matter. The reason I think so is that when I load the same activation in
both
tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface
in
tksurfer, save it, and load it in tkmedit, the point will land on
the
yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it,
and
load
it in tksurfer, they (tkmedit and tksurfer) show different
talairach
coordinates for the points. Question: what is the truth and what should I expect? Thanks, George
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
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
internally, tksurfer only uses the white surface vertex coords. A bit unfortunate, I agree.
doug
George He wrote:
Thanks Doug. I think I get the idea now. There is one thing that still bothers me though, which I described in my original email: suppose the same pial surface is loaded in tksurfer and tkmedit. If I click on the pial surface in tksurfer, save the point and load it in tkmedit, it always ends up on the white surface in tkmedit. Why not on the pial surface? (This has nothing to do with functional data overlay.) best, George
On Feb 6, 2008 2:07 PM, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
George He wrote:Hi, suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up?In theory, just the stuff in the middle, though usually the voxel size is so big that it gets both surfs. You can also use --interp trilinear to interpolate. You can also use --projfrac-avg to average across the ribbon.what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ?It will sample outside of the brain. dougThanks, George On Feb 6, 2008 1:33 PM, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf doug Bruce Fischl wrote: > Hi George, > > I'll leave this for Doug. I think the more standard stream is to use > mri_vol2surf to sample your fMRI volume onto the surface. It has > explicit parameters that control how you sample, but again once you've > sampled it you can display it on *any* surface and it will look the > same (white, pial, inflated, etc...) > > cheers, > Bruce > > > On Tue, 5 Feb 2008, George He wrote: > >> Hi Bruce, >> Thanks for your reply. The command I used to visualize is: >> tksurfer SUBJID rh inflated -overlay >> allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz >> \ >> -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ >> -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot >> what is the option to make the overlay displayed, say, on the pial >> surface, >> or on the face that is at the middle of the pial and the white surface? >> (I don't see a sampling option in tksurfer help.) >> George >> >> >> On Feb 5, 2008 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >>> Hi George, >>> >>> there are two different questions here: (1) what anatomical boundary >>> does >>> each surface represent, and (2) how do you sample functional data onto >>> the surface. For (1) the pial surface is indeed the boundary between >>> gray >>> matter and CSF, but for (2) once you choose a sampling strategy >>> (anywhere >>> from gray/white out to pial) the fMRI data can be displayed on any >>> of the >>> surfaces simply as a visualization. Is that clear? >>> >>> Bruce >>> >>> >>> On Tue, 5 Feb 2008, George He wrote: >>> >>>> Hi freesurfer experts, >>>> It seems to me the pial surface should be the surface of gray matter, >>> >>> but >>> >>>> when I overlay functional activations on it, it seems to be surface of >>> >>> white >>> >>>> matter. >>>> The reason I think so is that when I load the same activation in both >>>> tksurfer and tkmedit, >>>> if I click on an activated area (or any point) on the pial surface in >>>> tksurfer, save it, and load it in tkmedit, the point will land on the >>>> yellow/green lines while the tksurfer and tkmedit show the same >>> >>> talairach >>> >>>> coordinate for the point. >>>> If I click on a point that is on the red line in tkmedit, save it, and >>> >>> load >>> >>>> it in tksurfer, they (tkmedit and tksurfer) show different talairach >>>> coordinates for the points. >>>> Question: what is the truth and what should I expect? >>>> Thanks, >>>> George >>>> >>> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I think you can use the -white <surface> to use a different surface I think.
On Wed, 6 Feb 2008, Doug Greve wrote:
internally, tksurfer only uses the white surface vertex coords. A bit unfortunate, I agree.
doug
George He wrote:
Thanks Doug. I think I get the idea now. There is one thing that still bothers me though, which I described in my original email: suppose the same pial surface is loaded in tksurfer and tkmedit. If I click on the pial surface in tksurfer, save the point and load it in tkmedit, it always ends up on the white surface in tkmedit. Why not on the pial surface? (This has nothing to do with functional data overlay.) best, George
On Feb 6, 2008 2:07 PM, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
George He wrote:Hi, suppose I use mri_vol2surf --projfrac 0.5 ..., will everything between the white surface and the middle of the cortical surfaces show up in my resulting surface, or only the stuff on the middle surface will show up?In theory, just the stuff in the middle, though usually the voxel size is so big that it gets both surfs. You can also use --interp trilinear to interpolate. You can also use --projfrac-avg to average across the ribbon.what happens if I use mri_vol2surf --projfrac 0.5 --surf pial ... ?It will sample outside of the brain. dougThanks, George On Feb 6, 2008 1:33 PM, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Yea, tksurfer does not allow you to control the sampling distance. To do this, use mri_vol2surf doug Bruce Fischl wrote: > Hi George, > > I'll leave this for Doug. I think the more standard stream is to use > mri_vol2surf to sample your fMRI volume onto the surface. It has > explicit parameters that control how you sample, but again once you've > sampled it you can display it on *any* surface and it will look the > same (white, pial, inflated, etc...) > > cheers, > Bruce > > > On Tue, 5 Feb 2008, George He wrote: > >> Hi Bruce, >> Thanks for your reply. The command I used to visualize is: >> tksurfer SUBJID rh inflated -overlay >> allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz >> \ >> -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ >> -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot >> what is the option to make the overlay displayed, say, on the pial >> surface, >> or on the face that is at the middle of the pial and the white surface? >> (I don't see a sampling option in tksurfer help.) >> George >> >> >> On Feb 5, 2008 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >>> Hi George, >>> >>> there are two different questions here: (1) what anatomical boundary >>> does >>> each surface represent, and (2) how do you sample functional data onto >>> the surface. For (1) the pial surface is indeed the boundary between >>> gray >>> matter and CSF, but for (2) once you choose a sampling strategy >>> (anywhere >>> from gray/white out to pial) the fMRI data can be displayed on any >>> of the >>> surfaces simply as a visualization. Is that clear? >>> >>> Bruce >>> >>> >>> On Tue, 5 Feb 2008, George He wrote: >>> >>>> Hi freesurfer experts, >>>> It seems to me the pial surface should be the surface of gray matter, >>> >>> but >>> >>>> when I overlay functional activations on it, it seems to be surface of >>> >>> white >>> >>>> matter. >>>> The reason I think so is that when I load the same activation in both >>>> tksurfer and tkmedit, >>>> if I click on an activated area (or any point) on the pial surface in >>>> tksurfer, save it, and load it in tkmedit, the point will land on the >>>> yellow/green lines while the tksurfer and tkmedit show the same >>> >>> talairach >>> >>>> coordinate for the point. >>>> If I click on a point that is on the red line in tkmedit, save it, and >>> >>> load >>> >>>> it in tksurfer, they (tkmedit and tksurfer) show different talairach >>>> coordinates for the points. >>>> Question: what is the truth and what should I expect? >>>> Thanks, >>>> George >>>> >>> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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George He