Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of my recons which finished with no errors. I am reviwing the data and I see a lot of holes in the brain stem, Are these needs to be filled manually. Do you recommend to fill this type of holes or just the ones in the hemispheric white matter?
Thanks in advance John
nope, that shouldn't matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and coil elements, and hence low SNR causing this to happen.
cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote:
Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of my recons which finished with no errors. I am reviwing the data and I see a lot of holes in the brain stem, Are these needs to be filled manually. Do you recommend to fill this type of holes or just the ones in the hemispheric white matter?
Thanks in advance John
Dear Dr Bruce, Thank you very much for the response.
Kindly I have one additional question and I highly appreciate your answer! Attached is snapshot for the same subject (orig.mgz and wm.mgz) there are projections og white matter int he cortex. Do I need to erase these projections. Then runt he command recon-all -s <subject> -autorecon2-wm -autorecon3
Is this correct? I apologies if my questions are simple. I am beginner and this is my first manual edit!
-------- Original Message -------- Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:09 AM UTC Time: August 25, 2017 2:09 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
nope, that shouldn"t matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and coil elements, and hence low SNR causing this to happen.
cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote:
Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of my recons which finished with no errors. I am reviwing the data and I see a lot of holes in the brain stem, Are these needs to be filled manually. Do you recommend to fill this type of holes or just the ones in the hemispheric white matter?
Thanks in advance John
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 John
I'm not entirely certain what you mean, but the figure you sent looked fine. If you are thinking that the circled area is a detached piece of wm, it is almost certainly not. Click on the center of it and look in a different view and you will see that it is connected through-plane
cheers Bruce
On Fri, 25 Aug 2017, John Anderson wrote:
Dear Dr Bruce, Thank you very much for the response.
Kindly I have one additional question and I highly appreciate your answer! Attached is snapshot for the same subject (orig.mgz and wm.mgz) there are projections og white matter int he cortex. Do I need to erase these projections. Then runt he command recon-all -s <subject> -autorecon2-wm -autorecon3
Is this correct? I apologies if my questions are simple. I am beginner and this is my first manual edit!
-------- Original Message --------Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:09 AM UTC Time: August 25, 2017 2:09 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
nope, that shouldn"t matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and coil elements, and hence low SNR causing this to happen.
cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote:
Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of
my recons
which finished with no errors. I am reviwing the data and I see a
lot of
holes in the brain stem, Are these needs to be filled manually. Do
you
recommend to fill this type of holes or just the ones in the
hemispheric
white matter?
Thanks in advance John
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 Dr Bruce,
Yes it is in the blue circle. I point into it and I checked the other sections. Kindly see attached.
Thank you for the advice
-------- Original Message -------- Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:19 AM UTC Time: August 25, 2017 2:19 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
I"m not entirely certain what you mean, but the figure you sent looked fine. If you are thinking that the circled area is a detached piece of wm, it is almost certainly not. Click on the center of it and look in a different view and you will see that it is connected through-plane
cheers Bruce
On Fri, 25 Aug 2017, John Anderson wrote:
Dear Dr Bruce, Thank you very much for the response.
Kindly I have one additional question and I highly appreciate your answer! Attached is snapshot for the same subject (orig.mgz and wm.mgz) there are projections og white matter int he cortex. Do I need to erase these projections. Then runt he command recon-all -s <subject> -autorecon2-wm -autorecon3
Is this correct? I apologies if my questions are simple. I am beginner and this is my first manual edit!
-------- Original Message -------- Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:09 AM UTC Time: August 25, 2017 2:09 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
nope, that shouldn"t matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and coil elements, and hence low SNR causing this to happen.
cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote:
Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of
my recons
which finished with no errors. I am reviwing the data and I see a
lot of
holes in the brain stem, Are these needs to be filled manually. Do
you
recommend to fill this type of holes or just the ones in the
hemispheric
white matter?
Thanks in advance John
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, it's fine On Fri, 25 Aug 2017, John Anderson wrote:
Hi Dr Bruce,
Yes it is in the blue circle. I point into it and I checked the other sections. Kindly see attached.
Thank you for the advice
-------- Original Message --------Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:19 AM UTC Time: August 25, 2017 2:19 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
I"m not entirely certain what you mean, but the figure you sent looked fine. If you are thinking that the circled area is a detached piece of wm, it is almost certainly not. Click on the center of it and look in a different view and you will see that it is connected through-plane
cheers Bruce
On Fri, 25 Aug 2017, John Anderson wrote:
Dear Dr Bruce, Thank you very much for the response.
Kindly I have one additional question and I highly appreciate your
answer!
Attached is snapshot for the same subject (orig.mgz and wm.mgz)
there are
projections og white matter int he cortex. Do I need to erase these projections. Then runt he command recon-all -s <subject> -autorecon2-wm -autorecon3
Is this correct? I apologies if my questions are simple. I am beginner and this is my
first
manual edit!
-------- Original Message -------- Subject: Re: [Freesurfer] recon-all Local Time: August 25, 2017 10:09 AM UTC Time: August 25, 2017 2:09 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
nope, that shouldn"t matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and
coil
elements, and hence low SNR causing this to happen.
cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote:
Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of
my recons
which finished with no errors. I am reviwing the data and I see a
lot of
holes in the brain stem, Are these needs to be filled manually. Do
you
recommend to fill this type of holes or just the ones in the
hemispheric
white matter?
Thanks in advance John
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
-
Bruce Fischl -
John Anderson