Re: [Freesurfer] Accounting for lesions misclassified as non-brain matter
I tried editing the apar.2009a.aseg vpolume using 77 to fill in the lesions,
ran this code: recon-all -s ${subject} -autorecon2-cp this did not make any
difference.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
jennifer.fer...@alumni.ubc.ca [jennifer.fer...@alumni.ubc.ca]
Sent: Tuesday, March 31, 2015 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Accounting for lesions misclassified as non-brain
matter
From: jennifer.fer...@alumni.ubc.ca
Sent: Tuesday, March 31, 2015 11:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Accounting for lesions misclassified as non-brain matter
Hi there,
I am having an issue with stroke lesions that border onto the cortex being
misclassfied by freesurfer. Often with lesions in this region the pial boudary
gets dragged to surround the lesion, missing actual grey matter and
inaccurately classifying the tissue.
The trouble is that every fix I can think of does nothing to impact this
misclassification.
I have tried:
filling in the lesion on wm.mgz (pictured here)
filling it in with voxels set to 110 on brainmask.mgz
and filling it in with voxels set to 77 (wm hypointensities) on apar.mgz
yet still this problem persists. Are there any other fixes I can use to correct
this issue?
Alternately if this issue can't be corrected should I expect it to impact my
data much? These lesions typically occur in the insula, but I am only
interested in quantifying primary motor and sensory areas, so will the
estimation of volumes in these areas still be accurate?
Thanks for any insight anyone can provide!
- Jenn
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Re: [Freesurfer] Accounting for lesions misclassified as non-brain matter
Hi Jenn have you tried filling the lesions on the aseg.mgz before creating the surfaces? Bruce On Tue, 31 Mar 2015, jennifer.fer...@alumni.ubc.ca wrote: > > > From: jennifer.fer...@alumni.ubc.ca > Sent: Tuesday, March 31, 2015 11:04 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Accounting for lesions misclassified as non-brain matter > > Hi there, > I am having an issue with stroke lesions that border onto the cortex being > misclassfied by freesurfer. Often with lesions in this region the pial > boudary gets dragged to surround the lesion, missing actual grey matter and > inaccurately classifying the tissue. > The trouble is that every fix I can think of does nothing to impact this > misclassification. > I have tried: > filling in the lesion on wm.mgz (pictured here) > filling it in with voxels set to 110 on brainmask.mgz > and filling it in with voxels set to 77 (wm hypointensities) on apar.mgz > yet still this problem persists. Are there any other fixes I can use to > correct this issue? > Alternately if this issue can't be corrected should I expect it to impact my > data much? These lesions typically occur in the insula, but I am only > interested in quantifying primary motor and sensory areas, so will the > estimation of volumes in these areas still be accurate? > > Thanks for any insight anyone can provide! > - Jenn > > > ___ 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.
Re: [Freesurfer] Accounting for lesions misclassified as non-brain matter
From: jennifer.fer...@alumni.ubc.ca Sent: Tuesday, March 31, 2015 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Accounting for lesions misclassified as non-brain matter Hi there, I am having an issue with stroke lesions that border onto the cortex being misclassfied by freesurfer. Often with lesions in this region the pial boudary gets dragged to surround the lesion, missing actual grey matter and inaccurately classifying the tissue. The trouble is that every fix I can think of does nothing to impact this misclassification. I have tried: filling in the lesion on wm.mgz (pictured here) filling it in with voxels set to 110 on brainmask.mgz and filling it in with voxels set to 77 (wm hypointensities) on apar.mgz yet still this problem persists. Are there any other fixes I can use to correct this issue? Alternately if this issue can't be corrected should I expect it to impact my data much? These lesions typically occur in the insula, but I am only interested in quantifying primary motor and sensory areas, so will the estimation of volumes in these areas still be accurate? Thanks for any insight anyone can provide! - Jenn ___ 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.
