Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn
Hi Martijn, What does the wm.mgz look like in that area? Have you tried making any white matter edits? -Louis
On Mon, 12 Mar 2012, Martijn Steenwijk wrote:
Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn
Hi Martijn:
In our lab, we basically add a greater density of control points - almost 1 CP for every 2 voxels. This way the corrected pial looks closer to what's expected.
best,
Alan
BIDMC
On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk < martijnsteenwijk@gmail.com> wrote:
Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn
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@ Louis, no I didn't correct the WM mask yet. But since it's a step clearly 'behind' correcting the skull strip and adding control points, and it takes a lot of work to accurately draw the WM mask, I would prefer to automate things as much as possible...
@Alan, thanks for your suggestion - although 1 CP for 2 voxels appears to be a lot. Tomorrow I'll check whether adding CP's helps.
On Mon, Mar 12, 2012 at 3:47 PM, Alan Francis alandarkenergy@gmail.comwrote:
Hi Martijn:
In our lab, we basically add a greater density of control points - almost 1 CP for every 2 voxels. This way the corrected pial looks closer to what's expected.
best,
Alan
BIDMC
On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk < martijnsteenwijk@gmail.com> wrote:
Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn
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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.
Although the white surface finds its place based on intensity, it's starting point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you mention, drawing in some voxels combined with the intensity changes that come from the control points may help. Allison
On Mar 12, 2012, at 6:53 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
@ Louis, no I didn't correct the WM mask yet. But since it's a step clearly 'behind' correcting the skull strip and adding control points, and it takes a lot of work to accurately draw the WM mask, I would prefer to automate things as much as possible...
@Alan, thanks for your suggestion - although 1 CP for 2 voxels appears to be a lot. Tomorrow I'll check whether adding CP's helps.
On Mon, Mar 12, 2012 at 3:47 PM, Alan Francis alandarkenergy@gmail.com wrote: Hi Martijn:
In our lab, we basically add a greater density of control points - almost 1 CP for every 2 voxels. This way the corrected pial looks closer to what's expected.
best,
Alan
BIDMC
On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote: Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn
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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
If you upload it, we will take a look. Seems likely it is a topology fixing problem Cheers Bruce
On Mar 12, 2012, at 5:38 AM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
Dear all,
I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).
Best, Martijn <example.PNG> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
Allison Stevens Player -
Bruce Fischl -
Louis Nicholas Vinke -
Martijn Steenwijk