External Email - Use Caution
To whom it may concern:
I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:
External Email - Use Caution
To whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
External Email - Use Caution
Hi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need. -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:
External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
we got it. I'm out of town but will try to look at it soon cheers Bruce On Mon, 29 Jul 2019, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug,
Yes that is exactly the concern that we have.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Tuesday, July 30, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello Freesurfer team,
I have actually the same problem for many of my subjects. (see screenshots) Could you give me some recommendation for the intensity bounds for my subjects?
Best Carolin
[image: Screen Shot 2019-07-30 at 12.18.32 PM.png] [image: Screen Shot 2019-07-30 at 12.09.01 PM.png]
On Tue, Jul 30, 2019 at 10:53 AM Brian Biekman Brian.Biekman@times.uh.edu wrote:
External Email - Use CautionHi Doug,
Yes that is exactly the concern that we have.-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Tuesday, July 30, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File
Drop. Let me know if there is anything else you need.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where
the white matter
surface extends into the gray matter, especially in the parietal and
posterior temporal
regions. This is caused by the wm.mgz including too much gray matter.
This issue occurs to
some degree in every subject's scans. This can be fixed with extensive
wm volume edits but
since this appears to be a systematic problem, I wanted to find a
solution that could be
applied to every subject, possibly in the recon-all pipeline. I've
tried using an expert
parameters 2 different ways to no avail. I've changed the -wlo values
in mri_segment but it
removes wm voxels in the temporal lobe from the wm.mgz surface. I've
tried adding the
-prune and -gentle flags to mri_normalize but that appears to make the
problem worse. Is
there a better approach to try? If necessary, I can send a subject's
recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
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
External Email - Use Caution
Hi Doug, I just wanted to follow up on this last message I sent. What do you suggest that we do about the spots where the white surface "leaks" in the gray surface? -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
________________________________________ From: Brian Biekman Sent: Tuesday, July 30, 2019 12:51 PM To: Freesurfer support list Subject: RE: [Freesurfer] WM surface including too much gray matter
Hi Doug,
Yes that is exactly the concern that we have.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Tuesday, July 30, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In general, this would be handled by manual editing, but we are looking into whether a parameter adjustment can be used instead. The problem is that adjustments often result in underlabeling in other places.
On 8/5/2019 1:53 PM, Brian Biekman wrote:
External Email - Use CautionHi Doug, I just wanted to follow up on this last message I sent. What do you suggest that we do about the spots where the white surface "leaks" in the gray surface?
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: Brian Biekman Sent: Tuesday, July 30, 2019 12:51 PM To: Freesurfer support list Subject: RE: [Freesurfer] WM surface including too much gray matter
Hi Doug,
Yes that is exactly the concern that we have.-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Tuesday, July 30, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
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
External Email - Use Caution
Got it, thank you for your help, Doug! -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Monday, August 05, 2019 1:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
In general, this would be handled by manual editing, but we are looking into whether a parameter adjustment can be used instead. The problem is that adjustments often result in underlabeling in other places.
On 8/5/2019 1:53 PM, Brian Biekman wrote:
External Email - Use CautionHi Doug, I just wanted to follow up on this last message I sent. What do you suggest that we do about the spots where the white surface "leaks" in the gray surface?
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: Brian Biekman Sent: Tuesday, July 30, 2019 12:51 PM To: Freesurfer support list Subject: RE: [Freesurfer] WM surface including too much gray matter
Hi Doug,
Yes that is exactly the concern that we have.-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Tuesday, July 30, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the surface placement is accurate. I do find a few places where the white surface "leaks" into the cortex like in the attached picture just to the left of the cursor. Is this the type of thing you are worried about? If not, please send a pic of your concern. doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
External Email - Use CautionHi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let me know if there is anything else you need.
Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 29, 2019 9:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian
usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some
cheers Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:External Email - Use CautionTo whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output.
-- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman@uh.edu Brian.Biekman@times.uh.edu
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Brian Biekman -
Bruce Fischl -
Caroline Chwiesko -
Greve, Douglas N.,Ph.D.