Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar
Hi Caspar
try putting control points in the white matter where the pial surface doesn't get out far enough.
cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar
Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)? Caspar
On Thursday, October 3, 2013, Bruce Fischl wrote:
Hi Caspar
try putting control points in the white matter where the pial surface doesn't get out far enough.
cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Freesurfer Experts,
I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar
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/**compliancelinehttp://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.
is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain)
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar
On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar
try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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.
the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain)
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
Thanks, Bruce. The problem is fairly extensive. There is no way to do
normalize grey matter intensity (the white surface looks pretty good)?Caspar
On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar
try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain)
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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.
This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
hmmmm. Can you tell us more about the acquisition?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least
in the center of the wm, the voxels are almost all 110. caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain)
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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.
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
what resolution?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized
for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
Hi Caspar,
that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better? Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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.
Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar,
that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better?
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
Hi Bruce, another update: I now set more than 2000 control points which significantly improved the pial surface. I am still fighting with a few places though, in particular medially and orbitofrontal. I attached a screenshot of the problem that I am facing medially. Is this a situation where even more control points can help? Orbitofrontally, the issue seems to be that I cannot clearly discern white matter from some point on, so there is nothing to grow out from Caspar
2013/10/3 Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu
Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar,
that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better?
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near the pial surface that are probably part of your problem, and the images even in the zoom look really inhomogenous. I don't think we ever have to add thousands of control points, but I have no experiences with NHP data.
cheers Bruce
On Fri, 4 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce, another update: I now set more than 2000 control points which significantly improved the pial surface. I am still fighting with a few places though, in particular medially and orbitofrontal. I attached a screenshot of the problem that I am facing medially. Is this a situation where even more control points can help? Orbitofrontally, the issue seems to be that I cannot clearly discern white matter from some point on, so there is nothing to grow out from Caspar
2013/10/3 Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar,
that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better? Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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.
Hi Bruce, it sounds very possible that the bright spots (which are gadolinium-enhanced blood vessels) cause the problem. I guess I will have to remove them. Does it make sense to manually delete them from brain.mgz? Caspar
2013/10/7 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near the pial surface that are probably part of your problem, and the images even in the zoom look really inhomogenous. I don't think we ever have to add thousands of control points, but I have no experiences with NHP data.
cheers Bruce
On Fri, 4 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
another update: I now set more than 2000 control points which significantly improved the pial surface. I am still fighting with a few places though, in particular medially and orbitofrontal. I attached a screenshot of the problem that I am facing medially. Is this a situation where even more control points can help? Orbitofrontally, the issue seems to be that I cannot clearly discern white matter from some point on, so there is nothing to grow out from Caspar
2013/10/3 Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar
2013/10/3 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar,
that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better? Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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<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.
if you can On Mon, 7 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce, it sounds very possible that the bright spots (which are gadolinium-enhanced blood vessels) cause the problem. I guess I will have to remove them. Does it make sense to manually delete them from brain.mgz? Caspar
2013/10/7 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near the pial surface that are probably part of your problem, and the images even in the zoom look really inhomogenous. I don't think we ever have to add thousands of control points, but I have no experiences with NHP data. cheers Bruce On Fri, 4 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, another update: I now set more than 2000 control points which significantly improved the pial surface. I am still fighting with a few places though, in particular medially and orbitofrontal. I attached a screenshot of the problem that I am facing medially. Is this a situation where even more control points can help? Orbitofrontally, the issue seems to be that I cannot clearly discern white matter from some point on, so there is nothing to grow out from Caspar 2013/10/3 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu> Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar, that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better? Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> hmmmm. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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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