Good morning,
I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial?
Thank you kindly in advance,
Julia Hill
Julia Hill Research Assistant School of Psychiatry University of New South Wales
Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning,
I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial?
Thank you kindly in advance,
Julia Hill
Julia Hill Research Assistant
School of Psychiatry
University of New South Wales
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
if they are coincident then it is accurately detected as non-cortical and won't affect any thickness/volume corrections, so fixing it is really just aesthetic.
cheer Bruce
On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning, I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial? Thank you kindly in advance, Julia Hill Julia Hill Research Assistant School of Psychiatry University of New South Wales[IMAGE]
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a prominence, right? In that case it will only look better for results' displaying.
Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
if they are coincident then it is accurately detected as non-cortical and won't affect any thickness/volume corrections, so fixing it is really just aesthetic.
cheer Bruce
On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning, I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial? Thank you kindly in advance, Julia Hill Julia Hill Research Assistant School of Psychiatry University of New South Wales[IMAGE]
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
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.
yes, exactly. it will have a tiny effect on total surface area, but that includes noncortical regions anyway On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a prominence, right? In that case it will only look better for results' displaying.
Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
if they are coincident then it is accurately detected as non-cortical and won't affect any thickness/volume corrections, so fixing it is really just aesthetic.
cheer Bruce
On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning, I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial? Thank you kindly in advance, Julia Hill Julia Hill Research Assistant School of Psychiatry University of New South Wales[IMAGE]
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
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.
Since it is such a straightforward correction, I've been making it because I thought that it would have some effect (though tiny).
Thanks! Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
yes, exactly. it will have a tiny effect on total surface area, but that includes noncortical regions anyway On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a prominence, right? In that case it will only look better for results' displaying.
Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
if they are coincident then it is accurately detected as non-cortical and won't affect any thickness/volume corrections, so fixing it is really just aesthetic.
cheer Bruce
On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning,
I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial?
Thank you kindly in advance,
Julia Hill
Julia Hill Research Assistant
School of Psychiatry
University of New South Wales
[IMAGE]
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
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.
Great, thank you so much for your help!
Julia
Julia Hill Research Assistant School of Psychiatry University of New South Wales
Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
----- Original Message -----
From: " andreia " _andreia_@sapo.pt To: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Cc: "Julia Hill" julia.hill@neura.edu.au, freesurfer@nmr.mgh.harvard.edu Sent: Friday, 17 February, 2012 1:01:06 AM Subject: Re: [Freesurfer] optic nerve inlcuded as pial matter
Since it is such a straightforward correction, I've been making it because I thought that it would have some effect (though tiny).
Thanks! Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
yes, exactly. it will have a tiny effect on total surface area, but that includes noncortical regions anyway On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a prominence, right? In that case it will only look better for results' displaying.
Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
if they are coincident then it is accurately detected as non-cortical and won't affect any thickness/volume corrections, so fixing it is really just aesthetic.
cheer Bruce
On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.
After this I run recon-all -autorecon2-wm -autorecon3.
Cheers, Andreia
Citando Julia Hill julia.hill@neura.edu.au:
Good morning,
I have a question about editing of the pial. I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot). This occurs from between 5 and 10 slices in length. Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial?
Thank you kindly in advance,
Julia Hill
Julia Hill Research Assistant
School of Psychiatry
University of New South Wales
[IMAGE]
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
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@nmr.mgh.harvard.edu
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_andreia_＠sapo.pt -
Bruce Fischl -
Julia Hill