Re: [Freesurfer] wm-hypointensities variables
Thank you.
Yes, I mean, I can find in literature several methods
to estimate T1w and T2w lesion volumes. I guess the ones estimated from
FS are the sum of these non-wm- and wm- hypointensities values (and not
just wm-hypointensities), and are referred as T1w lesion volumes since
the segmentation was based on T1w images.
Usually in healthy subjects
nobody refers any value (in literature), so I suppose that authors just
ignore the fact that FS has estimates of this measure also for controls
(even if it's False Positive, or other reason).
Cheers
Em 2016-02-13
21:03, Bruce Fischl escreveu:
> It depends what you want. If you want
total volume, then yes. They are
> typically false positives in young
healthy subjects. Telling damaged
> white matter from say the
superior-most aspect of the caudate is *very*
> hard on just a T1
> On
Sat, 13 Feb 2016, Otília wrote:
>
>> Thank you for your reply. I just
wasn't expecting ("high") values in healthy subjects. Of course FS just
"sees" voxels, whether it's a lesion or other thing, but I was afraid it
would be some segmentation issue. I have also other MRI contrasts but I
really wanted to estimate possible T1w lesion volumes. That's why I
asked for some references, and to understand the difference between
"wm-hypointensities" and "non-WM-hypointensities". Should I sum both
when referring to "T1w lesion volume"? best regards Em 2016-02-11 17:30,
Bruce Fischl escreveu: you can turn this off with the -nowmsa flag I
believe in recon-all. The labels are for damaged white matter and
damaged gray matter, which can be tough to distinguish based only a T1.
We have some (not-yet-distributed) tools that do pretty well on this if
you have other contrasts like T2/FLAIR/PD. cheers Bruce On Thu, 11 Feb
2016, Otília wrote: Greetings, I am wondering if there is some
information regarding the meaning of "wm-hypointensities" and
"non-WM-hypointensities" variables from the aseg.stats file, ie, what
features are included in these variables and how FS computes them. I
checked previous posts that have the same issue I have now. I find some
non-zero, (some cases have "quite big") WM-hypointensities values for
healthy young brains. I find it odd. I would appreciate some additional
information about these issues. Thank you! Best regards,
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Re: [Freesurfer] wm-hypointensities variables
It depends what you want. If you want total volume, then yes. They are
typically false positives in young healthy subjects. Telling damaged
white matter from say the superior-most aspect of the caudate is *very*
hard on just a T1
On Sat, 13 Feb 2016, Otília wrote:
Thank you for your reply.
I just wasn't expecting ("high") values in healthy subjects. Of course FS
just "sees" voxels, whether it's a lesion or other thing, but I was afraid
it would be some segmentation issue. I have also other MRI contrasts but I
really wanted to estimate possible T1w lesion volumes.
That's why I asked for some references, and to understand the difference
between "wm-hypointensities” and “non-WM-hypointensities”. Should I sum both
when referring to "T1w lesion volume"?
best regards
Em 2016-02-11 17:30, Bruce Fischl escreveu:
you can turn this off with the -nowmsa flag I believe in recon-all. The
labels are for damaged white matter and damaged gray matter, which can be
tough to distinguish based only a T1. We have some (not-yet-distributed)
tools that do pretty well on this if you have other contrasts like
T2/FLAIR/PD.
cheers
Bruce
On Thu,
11 Feb 2016, Otília wrote:
Greetings, I am wondering if there is some
information regarding the meaning of
“wm-hypointensities” and “non-WM-hypointensities”
variables from the aseg.stats file, ie, what
features are included in these variables and how FS
computes them. I checked previous posts that have
the same issue I have now. I find some non-zero,
(some cases have “quite big”) WM-hypointensities
values for healthy young brains. I find it odd. I
would appreciate some additional information about
these issues. Thank you! Best regards,
___
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addressed. If you believe this e-mail was sent to you in error and the e-mai
l
contains patient information, please contact the Partners Compliance HelpLin
e at
http://www.partners.org/complianceline . If the e-mail was sent to you in er
ror
but does not contain patient information, please contact the sender and prop
erly
dispose of the e-mail.
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Re: [Freesurfer] wm-hypointensities variables
Thank you for your reply.
I just wasn't expecting ("high") values
in healthy subjects. Of course FS just "sees" voxels, whether it's a
lesion or other thing, but I was afraid it would be some segmentation
issue. I have also other MRI contrasts but I really wanted to estimate
possible T1w lesion volumes.
That's why I asked for some references,
and to understand the difference between "wm-hypointensities" and
"non-WM-hypointensities". Should I sum both when referring to "T1w
lesion volume"?
best regards
Em 2016-02-11 17:30, Bruce Fischl
escreveu:
> you can turn this off with the -nowmsa flag I believe in
recon-all. The
> labels are for damaged white matter and damaged gray
matter, which can be
> tough to distinguish based only a T1. We have
some (not-yet-distributed)
> tools that do pretty well on this if you
have other contrasts like
> T2/FLAIR/PD.
>
> cheers
> Bruce
>
> On
Thu,
> 11 Feb 2016, Otília wrote:
>
>> Greetings, I am wondering if
there is some information regarding the meaning of "wm-hypointensities"
and "non-WM-hypointensities" variables from the aseg.stats file, ie,
what features are included in these variables and how FS computes them.
I checked previous posts that have the same issue I have now. I find
some non-zero, (some cases have "quite big") WM-hypointensities values
for healthy young brains. I find it odd. I would appreciate some
additional information about these issues. Thank you! Best regards,
>
>
___
> Freesurfer mailing
list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [1]
>
>
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
[2] . 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.
Links:
--
[1]
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[2]
http://www.partners.org/complianceline
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.
Re: [Freesurfer] wm-hypointensities variables
you can turn this off with the -nowmsa flag I believe in recon-all. The labels are for damaged white matter and damaged gray matter, which can be tough to distinguish based only a T1. We have some (not-yet-distributed) tools that do pretty well on this if you have other contrasts like T2/FLAIR/PD. cheers Bruce On Thu, 11 Feb 2016, Otília wrote: Greetings, I am wondering if there is some information regarding the meaning of “wm-hypointensities” and “non-WM-hypointensities” variables from the aseg.stats file, ie, what features are included in these variables and how FS computes them. I checked previous posts that have the same issue I have now. I find some non-zero, (some cases have “quite big”) WM-hypointensities values for healthy young brains. I find it odd. I would appreciate some additional information about these issues. Thank you! Best regards, ___ 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.
[Freesurfer] wm-hypointensities variables
Greetings, I am wondering if there is some information regarding the meaning of "wm-hypointensities" and "non-WM-hypointensities" variables from the aseg.stats file, ie, what features are included in these variables and how FS computes them. I checked previous posts that have the same issue I have now. I find some non-zero, (some cases have "quite big") WM-hypointensities values for healthy young brains. I find it odd. I would appreciate some additional information about these issues. Thank you! Best regards, ___ 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.
