Hi guys,
I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum.
Attached is a pic of what I mean.[image: Inline image 1]
Thanks, Mike
Hi Michael
it's impossible to tell from the single slice whether that is correct or not. Cerebellum is also hard to give general advice about since it depends so critically on where you landmark. If you landmark too superiorly then the inferior parts of cerebellar cortex have large signal drop-off and we miss them. There are also muscles proximal to cerebellar cortex that look a light like gray matter.
Sorry I don't have anything more helpful to add Bruce
On Wed, 31 Jul 2013, Michael Kranz wrote:
Hi guys, I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum.
Attached is a pic of what I mean.Inline image 1
Thanks, Mike
Hi Michael,
It looks like lateral venous sinuses are included in this subject and as Bruce says, since the intensity is very close to cerebellar cortex, they are difficult to distinguish. It depends on what you are after in your analysis if you need to take care or not.
Regards,
Martin
Sent from my iPad
On 31.7.2013, at 23:23, Michael Kranz mbkranz@gmail.com wrote:
Hi guys,
I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum.
Attached is a pic of what I mean.<aseg.png>
Thanks, Mike _______________________________________________ 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.
Although the cerebellum isn't part of my primary analyses, I thought it would be interesting to compare cerebellum volume with my other subcortical measures (eg caudate and putamen) in predicting video game skill acquisition.
Also, I was flirting with the idea of using Buckner's cerebellum and striatum parcellations as well.
On Thu, Aug 1, 2013 at 8:22 AM, Martin Kavec martin.kavec@gmail.com wrote:
Hi Michael,
It looks like lateral venous sinuses are included in this subject and as Bruce says, since the intensity is very close to cerebellar cortex, they are difficult to distinguish. It depends on what you are after in your analysis if you need to take care or not.
Regards,
Martin
Sent from my iPad
On 31.7.2013, at 23:23, Michael Kranz mbkranz@gmail.com wrote:
Hi guys,
I was just wondering approximately how often the aseg volume will need
manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum.
Attached is a pic of what I mean.<aseg.png>
Thanks, Mike _______________________________________________ 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
contains patient information, please contact the Partners Compliance
HelpLine at
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Hi Michael
if you are trying to quantify cerebellar volume then you probably want to edit out these inaccuracies. If you just want to use Randy's stuff for e.g. seed analysis of rsFMRI then it won't make any difference
cheers Bruce
On Thu, 1 Aug 2013, Michael Kranz wrote:
Although the cerebellum isn't part of my primary analyses, I thought it would be interesting to compare cerebellum volume with my other subcortical measures (eg caudate and putamen) in predicting video game skill acquisition. Also, I was flirting with the idea of using Buckner's cerebellum and striatum parcellations as well.
On Thu, Aug 1, 2013 at 8:22 AM, Martin Kavec martin.kavec@gmail.com wrote: Hi Michael,
It looks like lateral venous sinuses are included in this subject and as Bruce says, since the intensity is very close to cerebellar cortex, they are difficult to distinguish. It depends on what you are after in your analysis if you need to take care or not. Regards, Martin Sent from my iPad On 31.7.2013, at 23:23, Michael Kranz <mbkranz@gmail.com> wrote: > Hi guys, > > I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum. >Attached is a pic of what I mean.<aseg.png>
Thanks, Mike _______________________________________________ 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
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dispose of the e-mail.
-- Michael Kranz Lab Manager | LBC Lab Beckman Institute University of Illinois 314-323-1329
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Michael Kranz