Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
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 Tanja
why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)?
cheers Bruce On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
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
Hello Bruce. Thank you for your reply.
I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure.
Tanja.
On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)?
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
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
it may also be the 8 channel coil, which can make things hard, particularly near the vertex. Dielectric effects are usually still pretty modest at 3T although they are visible. I think control points would be your best bet.
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hello Bruce. Thank you for your reply.
I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure.
Tanja.
On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)?
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
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
Do you think 32ch coil would be better? We also have data with the same scanner and same sequence, but 32ch coil. Although, visually, 32ch data is much more inhomogenious, especially in occipital part (it is too bright). We were afraid that wm there would be hard to distinguish from gm and that therefore the thickness would be too underestimated, that is why we decided to use 8ch data.
Tanja.
On Wed, Mar 28, 2012 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it may also be the 8 channel coil, which can make things hard, particularly near the vertex. Dielectric effects are usually still pretty modest at 3T although they are visible. I think control points would be your best bet.
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hello Bruce. Thank you for your reply.
I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure.
Tanja.
On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)?
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces?
Thank you, Tanja.
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
in our experience the 12 and 32 channel coils are much easier to process than the 8 channels, but it really depends on the coil geometry
Bruce On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Do you think 32ch coil would be better? We also have data with the same scanner and same sequence, but 32ch coil. Although, visually, 32ch data is much more inhomogenious, especially in occipital part (it is too bright). We were afraid that wm there would be hard to distinguish from gm and that therefore the thickness would be too underestimated, that is why we decided to use 8ch data.
Tanja.
On Wed, Mar 28, 2012 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it may also be the 8 channel coil, which can make things hard, particularly near the vertex. Dielectric effects are usually still pretty modest at 3T although they are visible. I think control points would be your best bet.
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hello Bruce. Thank you for your reply.
I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure.
Tanja.
On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)?
cheers Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
Hi Louis,
thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces.
Best wishes, Tanja.
On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis
On Tue, 27 Mar 2012, Tetiana Dadakova wrote:
> Dear FS list, > > After recon-all -all we had some wm missing in temporal part of the > brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all > -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. > wm_missing2, but the surfaces still look as fig. wm_missing1. > What can be the reason that wm.mgz edits didn't affect the surfaces? > > Thank you, > Tanja. >
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Louis Nicholas Vinke -
Tetiana Dadakova