Hi Freesurfer Experts and Antonin,
About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted. I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the commandrecon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong.At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips!Best Wishes,Shane
Dear Shane,
I would suggest to run:
recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg in case of such large ventricles.
Antonin Skoch
From: Shane Schofield shane.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@ikem.cz Sent: 4/22/2017 11:30 PM Subject: Filling in missing ventricles in WM
Hi Freesurfer Experts and Antonin,
About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted.
I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the command recon-all -s subject -autorecon2-wm -autorecon3
Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong.
At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz?
Appreciate your tips! Best Wishes, Shane
Thank you. I will try that. Do I run that command after editing the wm.mgz to fill in the ventricles? I noticed that the voxels (value = 255) are still 255 in the new WM.mgz after autorecon2-wm. Is this correct?
On Sunday, April 23, 2017 1:33 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Shane,
I would suggest to run:
recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg in case of such large ventricles.
Antonin Skoch
From: Shane Schofield shane.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@ikem.cz Sent: 4/22/2017 11:30 PM Subject: Filling in missing ventricles in WM
Hi Freesurfer Experts and Antonin,
About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted. I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the commandrecon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong.At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips!Best Wishes,Shane
yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg.
But as Antonin suggests, try running with -bigventricles and see if that fixes your problems
cheers Bruce
On Sun, 23 Apr 2017, Shane Schofield wrote:
Thank you. I will try that. Do I run that command after editing the wm.mgz to fill in the ventricles? I noticed that the voxels (value = 255) are still 255 in the new WM.mgz after autorecon2-wm. Is this correct?
On Sunday, April 23, 2017 1:33 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Shane,
I would suggest to run:
recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg in case of such large ventricles.
Antonin Skoch
From: Shane Schofield shane.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@ikem.cz Sent: 4/22/2017 11:30 PM Subject: Filling in missing ventricles in WM
Hi Freesurfer Experts and Antonin,About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted.
Inline image I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the command recon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong. Inline image At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips! Best Wishes, Shane
Hi Bruce, Thanks! The -bigventricles flag worked like a charm! But I have now run into other cases with fuzzy data and thin cortex that are not captured, such as the picture below:
Any tips on filing them out? Thank you.
On Sunday, April 23, 2017 3:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg.
But as Antonin suggests, try running with -bigventricles and see if that fixes your problems
cheers Bruce
On Sun, 23 Apr 2017, Shane Schofield wrote:
Thank you. I will try that. Do I run that command after editing the wm.mgz to fill in the ventricles? I noticed that the voxels (value = 255) are still 255 in the new WM.mgz after autorecon2-wm. Is this correct?
On Sunday, April 23, 2017 1:33 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Shane,
I would suggest to run:
recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg in case of such large ventricles.
Antonin Skoch
From: Shane Schofield shane.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@ikem.cz Sent: 4/22/2017 11:30 PM Subject: Filling in missing ventricles in WM
Hi Freesurfer Experts and Antonin,
About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted.
Inline image I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the command recon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong. Inline image At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips! Best Wishes, Shane
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Shane
I can't really tell from the image. YOu can try setting some of the intensity bounds in mris_make_surfaces and mri_segment (eg. wlo, ghi and such). If you upload the subject I'll take a look
cheers Bruce
On Wed, 26 Apr 2017, Shane Schofield wrote:
Hi Bruce,
Thanks!
The -bigventricles flag worked like a charm! But I have now run into other cases with fuzzy data and thin cortex that are not captured, such as the picture below:
Inline image
Any tips on filing them out?
Thank you.
On Sunday, April 23, 2017 3:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg.
But as Antonin suggests, try running with -bigventricles and see if that fixes your problems
cheers Bruce
On Sun, 23 Apr 2017, Shane Schofield wrote:
Thank you. I will try that. Do I run that command after editing the wm.mgz to fill in the ventricles? I noticed that the voxels (value = 255) are
still
255 in the new WM.mgz after autorecon2-wm. Is this correct?
On Sunday, April 23, 2017 1:33 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Shane,
I would suggest to run:
recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct
aseg
in case of such large ventricles.
Antonin Skoch
From: Shane Schofield shane.schofield@yahoo.com To: Freesurfer Support List freesurfer@nmr.mgh.harvard.edu, Antonin
Skoch
ansk@ikem.cz Sent: 4/22/2017 11:30 PM Subject: Filling in missing ventricles in WM
Hi Freesurfer Experts and Antonin,
About an earlier question on XL Defects
I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted.
Inline image I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the command recon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong. Inline image At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips! Best Wishes, Shane
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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