FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Where can I find more info on expert opts?
On Oct 28, 2013, at 6:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote:
Where can I find more info on expert opts?
On Oct 28, 2013, at 6:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Hi guys,
I am having a bit of trouble with expert options...
I ran:
recon-all -autorecon2 -autorecon3 -expert expert.opts -s <SUBJID>
my expert options file reads:
mri_segment -p 0.70
and recon-all exits with errors right after this output:
using 70% threshold mri_read(): couldn't determine type of file /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/s_100930ct/mri/0.70 mri_segment: could not read source volume from 0.70
What have I done incorrectly?
On Tue, Oct 29, 2013 at 2:25 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
https://surfer.nmr.mgh.**harvard.edu/fswiki/recon-all#**ExpertOptionsFilehttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote:
Where can I find more info on expert opts?
On Oct 28, 2013, at 6:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
By the way I’m also confused on what the effect of increasing/decreasing the mri_segment p threshold will have, I arbitrarily decided to lower the threshold but I’m not sure if that’s what I want On Oct 30, 2013, at 1:22 PM, Jonathan Holt whatsdac@umich.edu wrote:
Hi guys,
I am having a bit of trouble with expert options...
I ran:
recon-all -autorecon2 -autorecon3 -expert expert.opts -s <SUBJID>
my expert options file reads:
mri_segment -p 0.70
and recon-all exits with errors right after this output:
using 70% threshold mri_read(): couldn't determine type of file /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/s_100930ct/mri/0.70 mri_segment: could not read source volume from 0.70
What have I done incorrectly?
On Tue, Oct 29, 2013 at 2:25 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote:
Where can I find more info on expert opts?
On Oct 28, 2013, at 6:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whatsdac@umich.edu wrote:
FS experts,
both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?
Jon
<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jon
I would change the wm/gm/csf limits in mri_segment, not the pct thresh.
cheers Bruce On Wed, 30 Oct 2013, Jonathan Holt wrote:
By the way I?m also confused on what the effect of increasing/decreasing the mri_segment p threshold will have, I arbitrarily decided to lower the threshold but I?m not sure if that?s what I want On Oct 30, 2013, at 1:22 PM, Jonathan Holt whatsdac@umich.edu wrote:
Hi guys,I am having a bit of trouble with expert options...
I ran:
recon-all -autorecon2 -autorecon3 -expert expert.opts -s <SUBJID>
my expert options file reads:
mri_segment -p 0.70
and recon-all exits with errors right after this output:
using 70% threshold mri_read(): couldn't determine type of file /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/s_100930ct/mri/0.70 mri_segment: could not read source volume from 0.70
What have I done incorrectly?
On Tue, Oct 29, 2013 at 2:25 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote: Where can I find more info on expert opts? On Oct 28, 2013, at 6:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce On Oct 28, 2013, at 1:10 PM, Jonathan Holt <whatsdac@umich.edu> wrote: FS experts, both of these surfaces are incorrect and I?d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don?t seem to be an issue, though the problem area is incorrectly segmented as white matter. I?ve removed this segmentation and it?s still not alleviated the problem. How best to proceed? Jon <Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, duly noted.
In the mri_Segment help menu it gives defaults for hi/lo limits for gm and wm, are those intensity values?
If I wanted to keep empty space from being segmented as WM what exactly would I change?
Jon On Oct 30, 2013, at 2:14 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
I would change the wm/gm/csf limits in mri_segment, not the pct thresh.
cheers Bruce On Wed, 30 Oct 2013, Jonathan Holt wrote:
By the way I?m also confused on what the effect of increasing/decreasing the mri_segment p threshold will have, I arbitrarily decided to lower the threshold but I?m not sure if that?s what I want On Oct 30, 2013, at 1:22 PM, Jonathan Holt whatsdac@umich.edu wrote:
Hi guys,I am having a bit of trouble with expert options... I ran: recon-all -autorecon2 -autorecon3 -expert expert.opts -s <SUBJID> my expert options file reads: mri_segment -p 0.70 and recon-all exits with errors right after this output: using 70% threshold mri_read(): couldn't determine type of file /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/s_100930ct/mri/0.70 mri_segment: could not read source volume from 0.70 What have I done incorrectly? On Tue, Oct 29, 2013 at 2:25 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote: Where can I find more info on expert opts? On Oct 28, 2013, at 6:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Jon The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better Cheers Bruce On Oct 28, 2013, at 1:10 PM, Jonathan Holt <whatsdac@umich.edu> wrote: FS experts, both of these surfaces are incorrect and I?d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don?t seem to be an issue, though the problem area is incorrectly segmented as white matter. I?ve removed this segmentation and it?s still not alleviated the problem. How best to proceed? Jon <Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png> _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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