HI experts,
I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Louis,
thanks for your response. It’s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I’m trying to reduce the WM surface such that the empty space is not included. I’ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn’t work, the empty space is simply resegmented and the surface doesn’t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn’t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn’t worked…
I’m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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.
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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
Bruce,
If I understand you correctly, you’re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I’m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jon
maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote:
Bruce,
If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I?m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote:
Bruce,
If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I?m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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
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
Got it, I'll take a look.
On Mon, 4 Nov 2013, Jonathan Holt wrote:
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote:
Bruce,
If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I?m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
> HI experts, > > I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? > > Jon > _______________________________________________ > 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
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
Bruce,
If I understand you correctly, you’re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I’m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
Hey Louis,
thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running
recon-all -autorecon2-noaseg -subjid <SUBJID>
that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains.
Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked?
I?m open for ideas.
I should also note that this problem is not an issue in rh.orig.nofix
(sorry about duplicate email, Louis)
On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). -Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number?
Jon _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jonathan Holt -
Louis Nicholas Vinke