Re: [Freesurfer] WM Hypointensities

[Gopinath, Karthik]

External Email - Use Caution

Hi Andrew,

We do not currently support wm-hypointensities with recon-all-clinical runs. 
The synthseg based segmentation saved as aseg.mgz will not contain this label 
and thus your asset.stats has no information on this.

Karthik

On Jul 20, 2023, at 9:39 AM, Huang, Yujing  wrote:


External Email - Use Caution

You can try ‘—empty’ to see if it reports differently.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Thursday, July 20, 2023 9:38 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Gopinath, Karthik 
mailto:kgopin...@mgh.harvard.edu>>; Iglesias 
Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

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 is assigned in recon-all-clinical.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Dedinas Geoly
Sent: Wednesday, July 19, 2023 1:59 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

I ran the following as an example:

mri_segstats --seg 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/mri/aseg.mgz
 --ctab /Applications/freesurfer/7.4.0/FreeSurferColorLUT.txt --nonempty 
--excludeid 0 --sum 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/stats/aseg.stats


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, July 18, 2023 9:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

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?

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WM Hypointensities


External Email - Use Caution

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 supported by recon-all-clinical?

Best,
Andrew



---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine


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Re: [Freesurfer] WM Hypointensities

[Huang, Yujing]

External Email - Use Caution

You can try '-empty' to see if it reports differently.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Thursday, July 20, 2023 9:38 AM
To: Freesurfer support list 
Cc: Gopinath, Karthik ; Iglesias Gonzalez, Juan E. 

Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution
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 is assigned in recon-all-clinical.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Dedinas Geoly
Sent: Wednesday, July 19, 2023 1:59 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution
I ran the following as an example:


mri_segstats --seg 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/mri/aseg.mgz
 --ctab /Applications/freesurfer/7.4.0/FreeSurferColorLUT.txt --nonempty 
--excludeid 0 --sum 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/stats/aseg.stats


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, July 18, 2023 9:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

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?



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WM Hypointensities



External Email - Use Caution

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 supported by recon-all-clinical?



Best,

Andrew





---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine


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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] WM Hypointensities

[Huang, Yujing]

External Email - Use Caution

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 is assigned in recon-all-clinical.

Best,

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


External Email - Use Caution
I ran the following as an example:


mri_segstats --seg 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/mri/aseg.mgz
 --ctab /Applications/freesurfer/7.4.0/FreeSurferColorLUT.txt --nonempty 
--excludeid 0 --sum 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/stats/aseg.stats


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Tuesday, July 18, 2023 9:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

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?



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WM Hypointensities



External Email - Use Caution

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 supported by recon-all-clinical?



Best,

Andrew





---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine


___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] WM Hypointensities

[Andrew Dedinas Geoly]

External Email - Use Caution

I ran the following as an example:


mri_segstats --seg 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/mri/aseg.mgz
 --ctab /Applications/freesurfer/7.4.0/FreeSurferColorLUT.txt --nonempty 
--excludeid 0 --sum 
/Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/stats/aseg.stats


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Tuesday, July 18, 2023 9:40 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] WM Hypointensities


External Email - Use Caution

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?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WM Hypointensities



External Email - Use Caution

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 supported by recon-all-clinical?



Best,

Andrew





---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] WM Hypointensities

[Huang, Yujing]

External Email - Use Caution

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?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WM Hypointensities


External Email - Use Caution
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 supported by recon-all-clinical?

Best,
Andrew



---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine

___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] WM Hypointensities

[Andrew Dedinas Geoly]

External Email - Use Caution

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 supported by recon-all-clinical?

Best,
Andrew



---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] wm-hypointensities

[Andrew Dedinas Geoly]

External Email - Use Caution

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 supported by recon-all-clinical?

Best,
Andrew


---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine


___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] wm-hypointensities variables

[Otília]

 

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,
___ Freesurfer mailing list
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e-mail.
> 
> ___
>
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> 
>
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> addressed. If you believe this e-mail was sent to you in error
and the e-mail
> contains patient information, please contact the
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> http://www.partners.org/complianceline
[2] . If the e-mail was sent to you in error
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patient information, please contact the sender and properly
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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.

Re: [Freesurfer] wm-hypointensities variables

[Otília]

 

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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list
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> 
>
The information in this e-mail is intended only for the person to whom
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> addressed. If you believe this e-mail was sent to you in error
and the e-mail
> contains patient information, please contact the
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Re: [Freesurfer] wm-hypointensities variables

[Bruce Fischl]

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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ror
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erly
dispose of the e-mail.




 

 




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[Freesurfer] wm-hypointensities variables

[Otília]

 

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

[Bruce Fischl]

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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[Freesurfer] wm-hypointensities label on MS subjects

[Guido Orlando Pascariello]

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 PASCARIELLO
Facultad de Ingeniería - Universidad Nacional de Entre Ríos
Argentina
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Re: [Freesurfer] WM-hypointensities

[Douglas N Greve]

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


On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote:
 Thanks Doug,

 In my case I did as you said but as Bruce recommend use the wmparc, so 
 the voxels less than 4000, and = 5001 were left , and more than or 
 equal to 4000, and =5002 were right.

 So different approach but I think would be the same, isn't it?

 Can you explain to me how FS makes the PV correction on the output 
 volumes in aseg.stats?


 Best Regards,
 Gabriel.


 El 13/12/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:

 Gabriel, the way I've done it is to just assign WMSA to left or right 
 based on the column number of the WMSA voxel. If it is less than 128, 
 then it is right (78) if it is greater than 128 it is left (79). It's 
 not perfect, but it is correct in the vast majority of cases.
 doug


 On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote:
 Thanks Bruce,
 
 The problem is that for this set of subjects I only have the T1s, 
 anyways I would like to give a try onto the tools for WMSA, since I 
 have T2 from some subjects.
 
 On the other hand, If I'm right the way to do the assignment on 
 matlab, would be something like opening the mgz, finding their 
 positions and look which are the neighbors right?
 If so, I would like to not assign just the neighbor voxel, as this 
 might bias the assignment, I'm guessing that something like the 
 assignment done during the aparc+aseg.mgz creation (using GM 
 parcelation to map GM labels to the wm voxels - mri_aparc2aseg) 
 should be a correct way to do so. Can you point me to an article or 
 explain to me how this works indeed, and how the decision to the 
 belonging voxel is made, I think I know the basis, but not enough to 
 make my own script.
 
 If I do not understand bad, is something like, you take a voxel a 
 look to some contiguous voxels till you get into a point where all 
 the contiguous voxels are too far from the seed, and are surrounded 
 by lots of voxels belonging to other areas. I'm not quite sure about 
 the decision about when to stop the search. I really think that the 
 method like the implemented in the mri_apar2aseg is the perfect solution.
 
 Regards,
 Gabriel
 
 
 
 
 El 12/12/12, *Bruce Fischl * fis...@nmr.mgh.harvard.edu escribió:
 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 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,
 Gabriel
 
 
 El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:
   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 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.
   
   
 
 
   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.
 
 
 --
 --
 PhD. student Gabriel González-Escamilla
 Laboratory of Functional Neuroscience
 Department of Physiology, Anatomy, and Cell Biology
 University Pablo de Olavide
 Ctra. de Utrera, Km.1
 41013 - Seville
 - Spain -
 
 Email: ggon...@upo.es
 http://www.upo.es/neuroaging/es/
 
 
 --
 --
 PhD. student Gabriel González-Escamilla
 Laboratory of Functional Neuroscience
 Department of Physiology, Anatomy, and Cell Biology
 University Pablo de Olavide
 Ctra. de Utrera, Km.1
 41013 - Seville
 - Spain -
 
 Email: ggon...@upo.es
 http://www.upo.es/neuroaging/es/

 -- 
 Douglas N. 

Re: [Freesurfer] WM-hypointensities

[Gabriel Gonzalez Escamilla]

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 mean of the norm voxel intensities, do I need anything else?Could you tell me the formula to compute the PV?Kind Regards,Gabriel.El 17/12/12, Douglas N Greve  gr...@nmr.mgh.harvard.edu escribió: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.dougOn 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote: Thanks Doug, In my case I did as you said but as Bruce recommend use the wmparc, so  the voxels less than 4000, and = 5001 were left , and more than or  equal to 4000, and =5002 were right. So different approach but I think would be the same, isn't it? Can you explain to me how FS makes the PV correction on the output  volumes in aseg.stats? Best Regards, Gabriel. El 13/12/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Gabriel, the way I've done it is to just assign WMSA to left or right  based on the column number of the WMSA voxel. If it is less than 128,  then it is right (78) if it is greater than 128 it is left (79). It's  not perfect, but it is correct in the vast majority of cases. doug On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote: Thanks Bruce,  The problem is that for this set of subjects I only have the T1s,  anyways I would like to give a try onto the tools for WMSA, since I  have T2 from some subjects.  On the other hand, If I'm right the way to do the assignment on  matlab, would be something like opening the mgz, finding their  positions and look which are the neighbors right? If so, I would like to not assign just the neighbor voxel, as this  might bias the assignment, I'm guessing that something like the  assignment done during the aparc+aseg.mgz creation (using GM  parcelation to map GM labels to the wm voxels - mri_aparc2aseg)  should be a correct way to do so. Can you point me to an article or  explain to me how this works indeed, and how the decision to the  belonging voxel is made, I think I know the basis, but not enough to  make my own script.  If I do not understand bad, is something like, you take a voxel a  look to some contiguous voxels till you get into a point where all  the contiguous voxels are too far from the seed, and are surrounded  by lots of voxels belonging to other areas. I'm not quite sure about  the decision about when to stop the search. I really think that the  method like the implemented in the mri_apar2aseg is the perfect solution.  Regards, Gabriel El 12/12/12, *Bruce Fischl * fis...@nmr.mgh.harvard.edu escribió: 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 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, Gabriel   El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:   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 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.       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.   -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain -  Email: ggon...@upo.es 

Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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 between 
those two means.


cheers
Bruce


On Mon, 17 Dec 2012, Douglas N Greve 
wrote:




Sorry, I'll have to defer to Bruce, who wrote the code.
doug

On 12/17/2012 11:24 AM, Gabriel Gonzalez Escamilla wrote:

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 mean of the norm voxel intensities, do I
need anything else?

Could you tell me the formula to compute the PV?

Kind Regards,
Gabriel.




El 17/12/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:

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


On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote:

Thanks Doug,

In my case I did as you said but as Bruce recommend use the wmparc, so
the voxels less than 4000, and = 5001 were left , and more than or
equal to 4000, and =5002 were right.

So different approach but I think would be the same, isn't it?

Can you explain to me how FS makes the PV correction on the output
volumes in aseg.stats?


Best Regards,
Gabriel.


El 13/12/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:


Gabriel, the way I've done it is to just assign WMSA to left or right
based on the column number of the WMSA voxel. If it is less than 128,
then it is right (78) if it is greater than 128 it is left (79). It's
not perfect, but it is correct in the vast majority of cases.
doug


On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote:

Thanks Bruce,

The problem is that for this set of subjects I only have the T1s,

anyways I would like to give a try onto the tools for WMSA, since I
have T2 from some subjects.


On the other hand, If I'm right the way to do the assignment on

matlab, would be something like opening the mgz, finding their
positions and look which are the neighbors right?

If so, I would like to not assign just the neighbor voxel, as this

might bias the assignment, I'm guessing that something like the
assignment done during the aparc+aseg.mgz creation (using GM
parcelation to map GM labels to the wm voxels - mri_aparc2aseg)
should be a correct way to do so. Can you point me to an article or
explain to me how this works indeed, and how the decision to the
belonging voxel is made, I think I know the basis, but not enough to
make my own script.


If I do not understand bad, is something like, you take a voxel a

look to some contiguous voxels till you get into a point where all
the contiguous voxels are too far from the seed, and are surrounded
by lots of voxels belonging to other areas. I'm not quite sure about
the decision about when to stop the search. I really think that the
method like the implemented in the mri_apar2aseg is the perfect

solution.


Regards,
Gabriel




El 12/12/12, *Bruce Fischl * fis...@nmr.mgh.harvard.edu escribió:

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 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,
Gabriel


El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:
 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 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.




 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 

[Freesurfer] WM-hypointensities

[Gabriel Gonzalez Escamilla]

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.
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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.

Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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 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.
 

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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.

Re: [Freesurfer] WM-hypointensities

[Gabriel Gonzalez Escamilla]

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 Fischl  fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe 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.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: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 inthe 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.The information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] WM-hypointensities

[Gabriel Gonzalez Escamilla]

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  fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe 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.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:  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. ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] WM-hypointensities

[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 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,
Gabriel


El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:
  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 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.
  
  


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is
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e-mail
  contains patient information, please contact the Partners Compliance 
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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
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Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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 
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,
Gabriel



El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:
  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 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.
  
  
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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
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Re: [Freesurfer] WM-hypointensities

[Mary Ellen Koran]

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 Lab, Center for Human Genetics Research
 Vanderbilt University School of Medicine
 Duke University, Class of 2009, BSE
 Cell: 919.943.5114


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Re: [Freesurfer] WM-hypointensities

[Douglas N Greve]

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 segmentation analysis?

 Thanks!


 Mary Ellen Koran
 MD/PhD Candidate, MSTP
 Thornton-Wells Lab, Center for Human Genetics Research
 Vanderbilt University School of Medicine
 Duke University, Class of 2009, BSE
 Cell: 919.943.5114 tel:919.943.5114




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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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: 
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, MSTPThornton-Wells Lab, Center for Human Genetics
Research
Vanderbilt University School of Medicine
Duke University, Class of 2009, BSE
Cell: 919.943.5114



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Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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 subjects. For one subject in particular,
 there's a large purple-colored area labeled WM-hypointensities near
 the left caudate in aseg.mgz (see attached image) that looks to me
 like it should be labeled caudate instead (though I'll admit, I'm not
 an expert in neuroanatomy). I know that aseg.mgz is used in generating
 the statistics in aseg.stats, so I'm concerned that if I am correct
 the statistics I've been using are not accurate.

 Can anyone help me understand what these WM-hypointensities are and
 why there seems to be a large area labeled as such for this particular
 subject? Am I correct in assuming that an error of some kind may have
 occurred, and that this area should actually be labeled as caudate?

 Thanks,
 -Steve

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[Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...

[Gonzalo Rojas Costa]

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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Re: [Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...

[Douglas N Greve]

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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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling

[Bruce Fischl]

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:



 Another one mislabels nearly the entire CC at the center slice:



 Here you can see the light purple blotches above the caudate (light blue); 
 those are labeled as white matter hypointensities:



 And again here:



 The overall quality is not great, but we're trying to make the best of what 
 we have.  Any advice on correcting these common problems in our dataset 
 (apart from manually doctoring them) would be greatly appreciated!

 Warren

 On Oct 11, 2011, at 6:44 PM, Warren Winter 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 nearly the entire CC at the center slice:

 Screen shot 2011-10-11 at 6.21.35 PM.png

 You can see the light purple blotches above the caudate (light blue); those 
 are labeled as white matter hypointensities.

 Screen shot 2011-10-11 at 6.31.05 PM.png

 And again here:

 Screen shot 2011-10-11 at 6.20.18 PM.png

 The overall quality is not great, but we're trying to make the best of what 
 we have.  Any advice on correcting these common problems in our dataset 
 (apart from manually doctoring them) would be greatly appreciated!

 Warren

 On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote:

 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, 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 fixes that don't involve 
 manually doctoring the mislabelings
 (such as setting a particular flag for recon)?

 I am quite new to FS so please forgive any rudimentary misunderstandings.

 Thank you!

 Warren

 --
 Warren Winter
 Lab Coordinator
 Children's Hospital Boston
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224





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 e-mail
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 HelpLine at
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 error
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 properly
 dispose of the e-mail.




 --
 Warren Winter
 Research Coordinator
 Children's Hospital Boston
 Sheridan Laboratory of Cognitive Neuroscience
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224


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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling

[Bruce Fischl]

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 entire CC at the center slice:



 Here you can see the light purple blotches above the caudate (light blue); 
 those are labeled as white matter hypointensities:



 And again here:



 The overall quality is not great, but we're trying to make the best of what 
 we have.  Any advice on correcting these common problems in our dataset 
 (apart from manually doctoring them) would be greatly appreciated!

 Warren

 On Oct 11, 2011, at 6:44 PM, Warren Winter 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 nearly the entire CC at the center slice:

 Screen shot 2011-10-11 at 6.21.35 PM.png

 You can see the light purple blotches above the caudate (light blue); those 
 are labeled as white matter hypointensities.

 Screen shot 2011-10-11 at 6.31.05 PM.png

 And again here:

 Screen shot 2011-10-11 at 6.20.18 PM.png

 The overall quality is not great, but we're trying to make the best of what 
 we have.  Any advice on correcting these common problems in our dataset 
 (apart from manually doctoring them) would be greatly appreciated!

 Warren

 On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote:

 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, 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 fixes that don't involve 
 manually doctoring the mislabelings
 (such as setting a particular flag for recon)?

 I am quite new to FS so please forgive any rudimentary misunderstandings.

 Thank you!

 Warren

 --
 Warren Winter
 Lab Coordinator
 Children's Hospital Boston
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224





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 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.




 --
 Warren Winter
 Research Coordinator
 Children's Hospital Boston
 Sheridan Laboratory of Cognitive Neuroscience
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224


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[Freesurfer] WM hypointensities

[carolina.mr]

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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Re: [Freesurfer] WM hypointensities

[Bruce Fischl]

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 accurate, but 
it's not ready for distribution yet.

cheers
Bruce

On Tue, 11 Oct 2011, carolina.mr wrote:

 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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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling

[Bruce Fischl]

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 nearly the entire CC at the center slice: 
 
 Screen shot 2011-10-11 at 6.21.35 PM.png
 
 You can see the light purple blotches above the caudate (light blue); those 
 are labeled as white matter hypointensities.
 
 Screen shot 2011-10-11 at 6.31.05 PM.png
 
 And again here:
 
 Screen shot 2011-10-11 at 6.20.18 PM.png
 
 The overall quality is not great, but we're trying to make the best of what 
 we have.  Any advice on correcting these common problems in our dataset 
 (apart from manually doctoring them) would be greatly appreciated!
 
 Warren
 
 On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote:
 
 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, 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 fixes that don't involve manually 
 doctoring the mislabelings
 (such as setting a particular flag for recon)?
 
 I am quite new to FS so please forgive any rudimentary misunderstandings.
 
 Thank you!
 
 Warren
 
 --
 Warren Winter
 Lab Coordinator
 Children's Hospital Boston
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224
 
 
 
 
 
 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.
 
 
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[Freesurfer] WM hypointensities and corpus callosum mislabeling

[Warren Winter]

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 fixes that don't involve 
manually doctoring the mislabelings (such as setting a particular flag for 
recon)?

I am quite new to FS so please forgive any rudimentary misunderstandings.

Thank you!

Warren

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Lab Coordinator
Children's Hospital Boston
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224

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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling

[Bruce Fischl]

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, 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 fixes that don't involve manually 
doctoring the mislabelings
(such as setting a particular flag for recon)?

I am quite new to FS so please forgive any rudimentary misunderstandings.

Thank you!

Warren

--
Warren Winter
Lab Coordinator
Children's Hospital Boston
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224


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[Freesurfer] WM hypointensities in aseg vs wmparc

[Dankner, Nathan (NIH/NIMH) [F]]

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 visualize/label these in tkmedit?

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Re: [Freesurfer] WM hypointensities in aseg vs wmparc

[Douglas N Greve]

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 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 visualize/label 
 these in tkmedit?

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[Freesurfer] WM-hypointensities

[Anita di Iasio]

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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Re: [Freesurfer] WM-hypointensities

[Bruce Fischl]

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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