[Freesurfer] Editing pial surface and aseg
Dear FreeSurfer team I am correcting some structural MRI scans after the automated surface-based analysis and the automated segmentation. I would like to know if you have any information about how often the Voxel Edit is used and if it makes sense to correct the subcortical segmentation. I have identified specifically problems with the shape of the putamen and its borders, in some cases the shape of the putamen overlaps with the cortex. Additionally, if I am editing both the Pial and WM surfaces with "Recon Edit" and the subcortical segmentation with "Voxel Edit", after saving both changes can I run both analysis at the same time (recon-all -autorecon-pial -subjid AND recon-all -autorecon2-noaseg -autorecon3 -subjid)? Or do I need first to do, for example, Recon Edit, save the changes and run the analysis and then do Voxel Edit, save the changes and run the other analysis? 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Ubuntu 16.04 LTS Thank you very much in advance. Best regards, Lya Paas ___ 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] Editing Pial Surface
I'm wondering about how to best approach two similar problems with pial surfaces. In one case I'd like to extend it and in the other I'd like to reduce it (for lack of a better term) These first two images are from a brain in which I'd like to extend the surface. http://i.imgur.com/ziDQd.png http://i.imgur.com/i0sX3.png In this case focus on the bottom left and right corners of the cortex. You can see, especially in the second image (with aseg.mgz loaded), the pial surface cuts off part of the cortex on both sides. Interestingly, the pial surface seems to adhere to the aparc.mgz file, which is loaded and pretty clear in the first image, where the left out parts of the cortex are just labelled as 'none'. http://i.imgur.com/aUKiG.png http://i.imgur.com/4BRwv.png In the second case I want to edit the pial surface so it follows that gyrus toward the midline in the left hemisphere. In this case I've tried control points, specifically along the gyrus, and autorecon2-cp. I also tried to edit the parcellation along the gyrus for several slides followed by autorecon2 3. This didn't help anything, so I'm a bit stuck. You can see this brain follows the same trend as the last in which the pial surface follows the aparc.mgz, and the aseg.mgz seems more or less correct. Thanks and any help would be awesome! jon ___ 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.
Re: [Freesurfer] Editing Pial Surface
Hi Jon usually this happens because the wm in the wm.mgz doesn't extend out far enough. Is that the case here? If not, you can also try direct repositioning in freeview under tools-reposition surface. cheers Bruce p.s. we also have some newer tools that I've been working on that can use a flair or T2 image for this purpose, if you happen to have a high res one On Wed, 17 Oct 2012, Jonathan Holt wrote: I'm wondering about how to best approach two similar problems with pial surfaces. In one case I'd like to extend it and in the other I'd like to reduce it (for lack of a better term)These first two images are from a brain in which I'd like to extend the surface. http://i.imgur.com/ziDQd.png http://i.imgur.com/i0sX3.png In this case focus on the bottom left and right corners of the cortex. You can see, especially in the second image (with aseg.mgz loaded), the pial surface cuts off part of the cortex on both sides. Interestingly, the pial surface seems to adhere to the aparc.mgz file, which is loaded and pretty clear in the first image, where the left out parts of the cortex are just labelled as 'none'. http://i.imgur.com/aUKiG.png http://i.imgur.com/4BRwv.png In the second case I want to edit the pial surface so it follows that gyrus toward the midline in the left hemisphere. In this case I've tried control points, specifically along the gyrus, and autorecon2-cp. I also tried to edit the parcellation along the gyrus for several slides followed by autorecon2 3. This didn't help anything, so I'm a bit stuck. You can see this brain follows the same trend as the last in which the pial surface follows the aparc.mgz, and the aseg.mgz seems more or less correct. Thanks and any help would be awesome! jon ___ 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.
Re: [Freesurfer] Editing Pial Surface
And in your second set of images, you probably need to edit the wm.mgz. I suspect that there is a topology problem that is messing up the wm.orig cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 10/17/12 12:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon usually this happens because the wm in the wm.mgz doesn't extend out far enough. Is that the case here? If not, you can also try direct repositioning in freeview under tools-reposition surface. cheers Bruce p.s. we also have some newer tools that I've been working on that can use a flair or T2 image for this purpose, if you happen to have a high res one On Wed, 17 Oct 2012, Jonathan Holt wrote: I'm wondering about how to best approach two similar problems with pial surfaces. In one case I'd like to extend it and in the other I'd like to reduce it (for lack of a better term)These first two images are from a brain in which I'd like to extend the surface. http://i.imgur.com/ziDQd.png http://i.imgur.com/i0sX3.png In this case focus on the bottom left and right corners of the cortex. You can see, especially in the second image (with aseg.mgz loaded), the pial surface cuts off part of the cortex on both sides. Interestingly, the pial surface seems to adhere to the aparc.mgz file, which is loaded and pretty clear in the first image, where the left out parts of the cortex are just labelled as 'none'. http://i.imgur.com/aUKiG.png http://i.imgur.com/4BRwv.png In the second case I want to edit the pial surface so it follows that gyrus toward the midline in the left hemisphere. In this case I've tried control points, specifically along the gyrus, and autorecon2-cp. I also tried to edit the parcellation along the gyrus for several slides followed by autorecon2 3. This didn't help anything, so I'm a bit stuck. You can see this brain follows the same trend as the last in which the pial surface follows the aparc.mgz, and the aseg.mgz seems more or less correct. Thanks and any help would be awesome! jon ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] editing pial surface
Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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.
Re: [Freesurfer] editing pial surface
Hi Julia it's really hard to tell from just this image. If the problem is the skull strip removing voxels you can use the clone tool to paint them back in from another volume like the T1.mgz. Are you sure it's not dura or pial vessels? Where in the brain do you mean? cheers Bruce On Thu, 22 Mar 2012, Richter, Julia wrote: Sorry, this time with attachment :). Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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.
Re: [Freesurfer] editing pial surface
Hi Julia, Are you editing on a Mac? -Louis On Thu, 22 Mar 2012, Richter, Julia wrote: Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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 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.
Re: [Freesurfer] Editing pial surface
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a new pial surface (takes [a lot] less time).
thanks,
brian
On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:
Dear all,
I am trying to edit the pial surface by editing/deleting voxels in the
brain volume within the pial surface ('labeled' as a part of cortex), but
clearly are parts of dura when manually inspected. When I rerun the last
automatic procedures (fix, make_final, morph), and check the pial surface,
nothing has appeared to have changed. The voxels I deleted are gone,
though the pial surface still looks the same.
How can I fix this without having to regenerate/reconstruct all my
subjects? (I have approx. 100). Any tip?
I am by the way using the Freesurfer version from june (?) 2005, and due
to time restrictions I am not considering changing to the latest version
for this project.
Thanks a lot!
Best wishes,
Lars Tjelta Westlye
University of Oslo
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brian t. quinn
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Re: [Freesurfer] Editing pial surface
better to do it from inside recon-all so as to get it's bookkeeping. Run
with -finalsurfs
doug
Brian T. Quinn wrote:
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a new pial surface (takes [a lot] less time).
thanks,
brian
On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:
Dear all,
I am trying to edit the pial surface by editing/deleting voxels in the
brain volume within the pial surface ('labeled' as a part of cortex),
but
clearly are parts of dura when manually inspected. When I rerun the last
automatic procedures (fix, make_final, morph), and check the pial
surface,
nothing has appeared to have changed. The voxels I deleted are gone,
though the pial surface still looks the same.
How can I fix this without having to regenerate/reconstruct all my
subjects? (I have approx. 100). Any tip?
I am by the way using the Freesurfer version from june (?) 2005, and due
to time restrictions I am not considering changing to the latest version
for this project.
Thanks a lot!
Best wishes,
Lars Tjelta Westlye
University of Oslo
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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