External Email - Use Caution
Hello FreeSurfer experts,
I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions.
I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this?
I have attached an image of what the problem looks like below. Please let me know if you need anything else.
Thank you!
1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 2. Platform: macOS Mojave (version 10.14.6) 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64
[image: Screen Shot 2019-12-13 at 9.56.46 AM.png]
Hi Monica
hmmm, hard to say without seeing the dataset. You could try using expert options to change some of the intensity thresholds if this is something specific to your acquiisition. If you upload the gzipped subject dir we will take a look
cheers Bruce
On Fri, 13 Dec 2019, Monica Bondy wrote:
External Email - Use Caution
Hello FreeSurfer experts,
I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions.
I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this?
I have attached an image of what the problem looks like below. Please let me know if you need anything else.
Thank you!
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514
- Platform: macOS Mojave (version 10.14.6)
- uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019;
root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64
Screen Shot 2019-12-13 at 9.56.46 AM.png
Can you be clearer as to what the problem is? If it is that the cortical segmentation (red voxels) don't seem to follow the white/pial surfaces, then there is nothing to worry about because the aseg is not expected to have a good cortical segmentation (see aparc+aseg.mgz instead).
On 12/13/2019 12:12 PM, Monica Bondy wrote:
External Email - Use Caution
Hello FreeSurfer experts,
I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions.
I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this?
I have attached an image of what the problem looks like below. Please let me know if you need anything else.
Thank you!
1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 2. Platform: macOS Mojave (version 10.14.6) 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64
[Screen Shot 2019-12-13 at 9.56.46 AM.png]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Sorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't getting all of the gray matter. None of the threads have seem to been resolved so I hope I could get some help. Would it be alright if I sent the subject directory for you to take a look? Thank you.
On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Can you be clearer as to what the problem is? If it is that the cortical segmentation (red voxels) don't seem to follow the white/pial surfaces, then there is nothing to worry about because the aseg is not expected to have a good cortical segmentation (see aparc+aseg.mgz instead).
On 12/13/2019 12:12 PM, Monica Bondy wrote:
External Email - Use CautionHello FreeSurfer experts,
I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions.
I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this?
I have attached an image of what the problem looks like below. Please let me know if you need anything else.
Thank you!
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514
- Platform: macOS Mojave (version 10.14.6)
- uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat
Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64
[image: Screen Shot 2019-12-13 at 9.56.46 AM.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
It is hard to say from that image because of the aseg, but it looks like the white surface is not extending far enough and so the pial surface starts too far away to get all the way out. You might need some control points in the WM in that area
On 1/28/2020 7:56 PM, Monica Bondy wrote:
External Email - Use Caution
Sorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't getting all of the gray matter. None of the threads have seem to been resolved so I hope I could get some help. Would it be alright if I sent the subject directory for you to take a look? Thank you.
On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Can you be clearer as to what the problem is? If it is that the cortical segmentation (red voxels) don't seem to follow the white/pial surfaces, then there is nothing to worry about because the aseg is not expected to have a good cortical segmentation (see aparc+aseg.mgz instead). On 12/13/2019 12:12 PM, Monica Bondy wrote:External Email - Use Caution Hello FreeSurfer experts, I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions. I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this? I have attached an image of what the problem looks like below. Please let me know if you need anything else. Thank you! 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 2. Platform: macOS Mojave (version 10.14.6) 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 Screen Shot 2019-12-13 at 9.56.46 AM.png _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Thanks for getting back to me. I've recently asked for help in another thread and sent in the subject directory because the control points didn't work well after my attempt. But I'll take your advice and give it another try. Thank you!
On Fri, Jan 31, 2020 at 5:11 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It is hard to say from that image because of the aseg, but it looks like the white surface is not extending far enough and so the pial surface starts too far away to get all the way out. You might need some control points in the WM in that area
On 1/28/2020 7:56 PM, Monica Bondy wrote:
External Email - Use CautionSorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't getting all of the gray matter. None of the threads have seem to been resolved so I hope I could get some help. Would it be alright if I sent the subject directory for you to take a look? Thank you.
On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Can you be clearer as to what the problem is? If it is that the cortical segmentation (red voxels) don't seem to follow the white/pial surfaces, then there is nothing to worry about because the aseg is not expected to have a good cortical segmentation (see aparc+aseg.mgz instead).
On 12/13/2019 12:12 PM, Monica Bondy wrote:
External Email - Use CautionHello FreeSurfer experts,
I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions.
I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this?
I have attached an image of what the problem looks like below. Please let me know if you need anything else.
Thank you!
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514
- Platform: macOS Mojave (version 10.14.6)
- uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat
Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64
[image: Screen Shot 2019-12-13 at 9.56.46 AM.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
-
Bruce Fischl -
Douglas N. Greve -
Greve, Douglas N.,Ph.D.
-
Monica Bondy