alf Of Huang, Yujing
Sent: Thursday, July 20, 2023 9:38 AM
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Cc: Gopinath, Karthik
mailto:kgopin...@mgh.harvard.edu>>; Iglesias
Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Subject: Re: [
E.
Subject: Re: [Freesurfer] WM Hypointensities
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Hi Andrew,
I see you specified '-nonempty'. 'wm-hypointensity' is probably excluded
because the voxel count is zero. I'm only looking at this from programmer point
of view. I don't know how wm-hypointensity
,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andrew Dedinas Geoly
Sent: Wednesday, July 19, 2023 1:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] WM Hypointensities
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I ran the following as an example:
mri_segstats --seg
To: Freesurfer support list
Subject: Re: [Freesurfer] WM Hypointensities
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Hi Andrew,
I can’t answer if wm-hypointensity is supported in recon-all-clinical. I’m
assuming that you obtained aseg.stats by running mri_segstats. How does your
command look like
On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WM Hypointensities
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Hi Freesurfer experts!
I am hoping to extract the wm-hypointensity data from some recon-all-clinical
runs. I
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Hi Freesurfer experts!
I am hoping to extract the wm-hypointensity data from some recon-all-clinical
runs. I was able to extract aseg.stats information correctly but noticed there
was no information regarding the wm-hypointensities.
Is this
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Hi Freesurfer experts!
I am hoping to extract the wm-hypointensity data from some recon-all-clinical
runs. I was able to extract aseg.stats information correctly but noticed there
was no information regarding the wm-hypointensities.
Is this
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
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
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.
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
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
Hi FS Experts:
I've been using T1 data from MS subjects in order to try to identify lesion
volume using wm-hypointensities label from aseg.
I wonder if there is any tool which uses T2-flair sequence to the same goal?
I'll be grateful if you can help
Being all for now, I await a reply
Guido
The PV is done based on intensities. For each voxel an the boundary of
an ROI, the voxel intensity is assumed to be a weighted summation of the
the average intensities in each ROI. Knowing the average intensities in
the ROIs and the actual intensity of the voxel, the PV can be computed.
doug
OK the Doug, I know which are the voxels contained into a ROI. From all of them I know the norm.mgz and the brainmask.mgz values, because I'm assuming that FS always work with the brainmask.mgz to know the actual voxel intensity, as indicated when running mri_segstats.I can easily calculate the
Hi Gabriel
we find the mean of the label intensity in a region around the voxel in
question using voxels that don't border another label, then do the same
for the most common neighboring label that is different from the one in
question and compute the volume fraction assuming a linear mixing
Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel.
Hi Gabriel
we don't lateralize them by default, so look for WM_hypointensities (77)
instead. It would be pretty easy to lateralize them based on neighboring
labels.
cheers
Bruce
On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:
Dear Freesurfers,
I'm looking for a way to compute
Yes I did loo at the total WH-hypointensities(77), and substract them without a problem.What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS?Actually I'm interested in knowing to wich specific label o region they are.Bests,GabrielEl 12/12/12, Bruce
Thanks bruce, for your answer,Does it exist a tool on FS or matlab to do such asignment of voxels from the WM-hypointensities (77) to the neighbouring labels?If so, does it can use whoever the aseg.mgz,the aparc+aseg or the wmparc.mgz to do this asignment?Thanks,GabrielEl 12/12/12, Bruce Fischl
then I would either use TRACULA (if you have DWI) or the wmparc to generate
ROIs. I meant that you could count whether there are more lh or rh wm
labels neighboring each one to figure out which hemi they are in
cheers
Bruce
On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:
Yes I did
wmparc should do it I think, although we don't have any tools for doing
so it wouldn't be very hard in matlab
On Wed, 12 Dec 2012, Gabriel Gonzalez
Escamilla wrote:
Thanks bruce, for your answer,
Does it exist a tool on FS or matlab to do such asignment of voxels from the
Hi,
I'm responding to this archived email:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023599.html
Is it possible to run recon-all with the switch -nowmsa to get rid of the
white matter segmentation analysis?
Thanks!
Mary Ellen Koran
MD/PhD Candidate, MSTP
Thornton-Wells
Yes, you should be able to.
doug
On 08/10/2012 04:58 PM, Mary Ellen Koran wrote:
Hi,
I'm responding to this archived email:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023599.html
Is it possible to run recon-all with the switch -nowmsa to get rid of
the white matter
Hi Mary Ellen
yes, that will remove the wmsas. It won't actually skip any steps in the
analysis, but it will replace every wmsa label with the 2nd most probable
one.
cheers
Bruce
On Fri, 10 Aug 2012, Mary Ellen Koran wrote:
Hi,
I'm responding to this archived email:
Hi Steve
it's hard to tell from a single slice. You can disable the wmsa labeling
by giving mri_ca_label the switch -nowmsa
cheers
Bruce
On Tue, 1 May 2012, Steven
Korycinski wrote:
To all,
I've been using aseg.stats to gather volumetric data about size of the
left caudate for a group of
Hi:
In aseg.stats the WM hypointensities is included in left-cerebral
(right-cerebral) white matter volume ?...
Sincerely,
Gonzalo Rojas Costa
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yes
doug
Gonzalo Rojas Costa wrote:
Hi:
In aseg.stats the WM hypointensities is included in left-cerebral
(right-cerebral) white matter volume ?...
Sincerely,
Gonzalo Rojas Costa
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Hi Warren
it's always hard/impossible to diagnose from snapshots. Can you upload an
entire subject's dir to the file drop?
Bruce
On Wed, 12 Oct 2011, Warren Winter
wrote:
Let me try this again.
Here's one that mislabeled parts of the CC as left cerebral white matter at
the center slice:
p.s. the first one at least looks like so much subject motion that the
scan may not be usable
On Wed, 12 Oct 2011, Warren Winter wrote:
Let me try this again.
Here's one that mislabeled parts of the CC as left cerebral white matter at
the center slice:
Another one mislabels nearly the
Hello,
How can I describe the method for WM hypointhensities segmentation and volume calculation?
Can you suggest a reference?
Thank you, Carolina
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Hi Carolina,
the one that is the distributed version of freesurfer now uses the same
algorithm as the rest of the aseg labels except that no constraints on
connectivity/topology are applied. We are working on a new method that uses
multispectral (T2/PD/FLAIR) inputs and is considerably more
Hmmm, can you upload a couple of examples?
On Oct 11, 2011, at 6:44 PM, Warren Winter
warren.win...@childrens.harvard.edu wrote:
Here's one that mislabeled parts of the CC as left cerebral white matter at
the center slice:
Screen shot 2011-10-11 at 6.31.19 PM.png
Another one mislabels
Hello,
In a number of our subjects I've been finding white matter hypointensities
around the anterior edge of the caudate, as well as mislabelings of the corpus
callosum as cerebral white matter (at and/or around slice 128, sagittal). Has
anyone else encountered these problems, and are there
Hi Warren
can you send us some images to show us what you mean? Or upload an
example dataset for us to look at?
cheers
Bruce
On Mon, 10 Oct 2011, Warren Winter wrote:
Hello,
In a number of our subjects I've been finding white matter hypointensities
around the anterior edge of the caudate,
Hello all,
I was curious as to whether it is preferable to use the wm hypointensities
output from wmparc.stats or from aseg.stats or if there is no real difference.
Also, I believe I've seen this answered elsewhere, but just to be clear, is it
the case that there is currently no way to
Use the ones in aseg.stats. When you load aseg.mgz into tkmedit, the
hypo intensities show up as segmentations.
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I was curious as to whether it is preferable to use the wm hypointensities
output from wmparc.stats or from aseg.stats or if there
Hi all,
I don't kown what is WM-hypointensities
Is it a volume? I suppose this because WM-hypointensities is in the
aseg.stats.
thanks
Anita di Iasio
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they are voxels with abnormal appearing white matter
On Tue, 7 Jul 2009,
Anita di Iasio wrote:
Hi all,
I don't kown what is WM-hypointensities
Is it a volume? I suppose this because WM-hypointensities is in the
aseg.stats.
thanks
Anita di Iasio
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