Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question:
1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36?
2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong?
Thank you, Tetiana.
On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
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.
try disabling use of gcut by adding -no-gcut to the end of recon-all. sometimes it can cut too much (something thats fixed in the upcoming release).
n.
On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote:
Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question:
- Regarding mri_gcut: should I use the default intensity of 110 for
white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36?
- Regarding manual removing of some voxels: the 'Edit Voxels' tool
doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong?
Thank you, Tetiana.
On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
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
I attach a picture of what I get if I run
<recon-all -autorecon1 -subjid name_of_subj -no-gcut>.
I feel that I need to change the -T threshold of WM intensity, does it make sense? If I put this -T value to 0.5, the out-of-brain structures are cut, but I wonder how it affects the white matter.
Thank you, Tanja
On Wed, Feb 2, 2011 at 2:36 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
try disabling use of gcut by adding -no-gcut to the end of recon-all. sometimes it can cut too much (something thats fixed in the upcoming release).
n.
On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote:
Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question:
- Regarding mri_gcut: should I use the default intensity of 110 for
white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36?
- Regarding manual removing of some voxels: the 'Edit Voxels' tool
doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong?
Thank you, Tetiana.
On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
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
This is probably ok. Run it all the way through and see if it affects the surfaces. If not, you are all set
On Feb 2, 2011, at 10:30 AM, Tetiana Dadakova tetiana.d@gmail.com wrote:
I attach a picture of what I get if I run
<recon-all -autorecon1 -subjid name_of_subj -no-gcut>.
I feel that I need to change the -T threshold of WM intensity, does it make sense? If I put this -T value to 0.5, the out-of-brain structures are cut, but I wonder how it affects the white matter.
Thank you, Tanja
On Wed, Feb 2, 2011 at 2:36 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
try disabling use of gcut by adding -no-gcut to the end of recon-all. sometimes it can cut too much (something thats fixed in the upcoming release).
n.
On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote:
Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question:
- Regarding mri_gcut: should I use the default intensity of 110 for
white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36?
- Regarding manual removing of some voxels: the 'Edit Voxels' tool
doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong?
Thank you, Tetiana.
On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
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
<skull_strip.tiff>
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Nick Schmansky -
Tetiana Dadakova