Re: [Freesurfer] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl

I appreciate your explanation. Thank you.

Best Wishes,

Han

On Mon, Oct 3, 2016 at 11:37 AM, Bruce Fischl 
wrote:

> yes, I believe so
>
> On Mon, 3 Oct 2016, Hanbyul Cho wrote:
>
> Dear Bruce Fischl
>>
>> ?h.white.H,  ?h.curv, and H Mean reflected the vector fields with 'sign(+
>> or
>> -)', and MeanCurv reflected the integral of the 'absolute' value of mean
>> curvature.  Am I understanding this correctly?
>>
>> Best Wishes,
>>
>> Han
>>
>>
>> On Mon, Oct 3, 2016 at 7:49 AM, Bruce Fischl 
>> wrote:
>>   Hi Han
>>
>>   I'm not sure I understand you question. The sign of the
>>   curvature depends on the arbirary convention you choose for the
>>   normal vector field over the surface. We pick and outwards
>>   pointing normal, which means that gyral regions in general have
>>   negative curvature (since they lie 'below' the tangent plane in
>>   terms of their dot product with the normal) and sulcal ones are
>>   positive. AFAIK both the ?h.white.H and ?h.curv curvatures obey
>>   this convention, although the smoothing applied to the ?h.curv
>>   will mean that some places they will have different sign. If you
>>   plot them both you will see that they are pretty highly
>>   correlated though.
>>
>>   Does that answer your question? If not, can you clarify?
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Sun, 2 Oct 2016, Hanbyul Cho wrote:
>>
>> Dear FreeSurfer Team,
>>
>> I apologize for the repetitive questions.
>>
>> I made 2 labels which included bilateral paracentral
>> lobule and sulcus
>> regions.
>> Then I extract the values:
>>- MeanCurv
>>  After mris_anatomical_stats processing, I
>> extracted the MeanCurv by the
>> command,
>>   'aparcstats2table --hemi ?h --parc  --meas
>> meancurv --subjects
>>  --tablefile '
>>
>>- ?h.Curv
>>   After mris_anatomical_stats processing with
>> the option '-t lh.curv', I
>> extracted the curvature value by the command,
>>   'aparcstats2table --hemi ?h --parc  --meas
>> thickness--subjects
>>  --tablefile '
>>
>>   - H  +- ,   H Mean Rectified Surface
>> Integral
>> The Mean curvature values were compute by the
>> command,
>> 'mris_curvature_Stats -l  -g -n -m -f
>> white -o 
>>  ?h'
>>
>> I analyzed the each value. The ?h.Curv mean (within
>> the label) has opposite
>> relationship with Z value compared to MeanCurv,
>> while similar relationship
>> with Z value compared to H .
>>
>> I heard that the MeanCurv is the integral of the
>> rectified mean curvature of
>> white matter surface (1/r mm), and ?h.curv is the
>> mean curvature of the
>> white matter surface with a Gaussian smoothing
>> kernel applied.
>> It looks that the MeanCurv and H Mean Rectified
>> Surface Integral has only
>> positive values, while the H  and ?h.curv has
>> positive or negative
>> value.
>>
>> I wonder whether MeanCurv and ?h.curv has the
>> difference meaning or
>> difference formula.
>> And I would like to know the meaning of the ?h.curv
>> negative value.
>> Is H  ( by mris_curvature_Stats ) compute from
>> ?h.curv ?
>>
>>
>> Thank you.
>>
>> Han.
>>
>>
>>
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>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>> it is
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>> HelpLine at
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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Bruce Fischl]

yes, I believe so
On Mon, 3 Oct 2016, Hanbyul Cho wrote:


Dear Bruce Fischl

?h.white.H,  ?h.curv, and H Mean reflected the vector fields with 'sign(+ or
-)', and MeanCurv reflected the integral of the 'absolute' value of mean
curvature.  Am I understanding this correctly?

Best Wishes,

Han


On Mon, Oct 3, 2016 at 7:49 AM, Bruce Fischl 
wrote:
  Hi Han

  I'm not sure I understand you question. The sign of the
  curvature depends on the arbirary convention you choose for the
  normal vector field over the surface. We pick and outwards
  pointing normal, which means that gyral regions in general have
  negative curvature (since they lie 'below' the tangent plane in
  terms of their dot product with the normal) and sulcal ones are
  positive. AFAIK both the ?h.white.H and ?h.curv curvatures obey
  this convention, although the smoothing applied to the ?h.curv
  will mean that some places they will have different sign. If you
  plot them both you will see that they are pretty highly
  correlated though.

  Does that answer your question? If not, can you clarify?

  cheers
  Bruce



  On Sun, 2 Oct 2016, Hanbyul Cho wrote:

Dear FreeSurfer Team,

I apologize for the repetitive questions.

I made 2 labels which included bilateral paracentral
lobule and sulcus
regions.
Then I extract the values:  
   - MeanCurv
     After mris_anatomical_stats processing, I
extracted the MeanCurv by the
command,  
  'aparcstats2table --hemi ?h --parc  --meas
meancurv --subjects
 --tablefile '

   - ?h.Curv  
      After mris_anatomical_stats processing with
the option '-t lh.curv', I
extracted the curvature value by the command,
  'aparcstats2table --hemi ?h --parc  --meas
thickness--subjects
 --tablefile '

  - H  +- ,   H Mean Rectified Surface
Integral
    The Mean curvature values were compute by the
command,
    'mris_curvature_Stats -l  -g -n -m -f
white -o 
 ?h'

I analyzed the each value. The ?h.Curv mean (within
the label) has opposite
relationship with Z value compared to MeanCurv,
while similar relationship
with Z value compared to H .

I heard that the MeanCurv is the integral of the
rectified mean curvature of
white matter surface (1/r mm), and ?h.curv is the
mean curvature of the
white matter surface with a Gaussian smoothing
kernel applied.
It looks that the MeanCurv and H Mean Rectified
Surface Integral has only
positive values, while the H  and ?h.curv has
positive or negative
value.

I wonder whether MeanCurv and ?h.curv has the
difference meaning or
difference formula.
And I would like to know the meaning of the ?h.curv
negative value.
Is H  ( by mris_curvature_Stats ) compute from
?h.curv ?


Thank you.

Han.



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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl

?h.white.H,  ?h.curv, and H Mean reflected the vector fields with 'sign(+
or -)', and MeanCurv reflected the integral of the 'absolute' value of mean
curvature.
Am I understanding this correctly?

Best Wishes,

Han


On Mon, Oct 3, 2016 at 7:49 AM, Bruce Fischl 
wrote:

> Hi Han
>
> I'm not sure I understand you question. The sign of the curvature depends
> on the arbirary convention you choose for the normal vector field over the
> surface. We pick and outwards pointing normal, which means that gyral
> regions in general have negative curvature (since they lie 'below' the
> tangent plane in terms of their dot product with the normal) and sulcal
> ones are positive. AFAIK both the ?h.white.H and ?h.curv curvatures obey
> this convention, although the smoothing applied to the ?h.curv will mean
> that some places they will have different sign. If you plot them both you
> will see that they are pretty highly correlated though.
>
> Does that answer your question? If not, can you clarify?
>
> cheers
> Bruce
>
>
>
>
> On Sun, 2 Oct 2016, Hanbyul Cho wrote:
>
> Dear FreeSurfer Team,
>>
>> I apologize for the repetitive questions.
>>
>> I made 2 labels which included bilateral paracentral lobule and sulcus
>> regions.
>> Then I extract the values:
>>- MeanCurv
>>  After mris_anatomical_stats processing, I extracted the MeanCurv by
>> the
>> command,
>>   'aparcstats2table --hemi ?h --parc  --meas meancurv --subjects
>>  --tablefile '
>>
>>- ?h.Curv
>>   After mris_anatomical_stats processing with the option '-t
>> lh.curv', I
>> extracted the curvature value by the command,
>>   'aparcstats2table --hemi ?h --parc  --meas thickness--subjects
>>  --tablefile '
>>
>>   - H  +- ,   H Mean Rectified Surface Integral
>> The Mean curvature values were compute by the command,
>> 'mris_curvature_Stats -l  -g -n -m -f white -o 
>>  ?h'
>>
>> I analyzed the each value. The ?h.Curv mean (within the label) has
>> opposite
>> relationship with Z value compared to MeanCurv, while similar relationship
>> with Z value compared to H .
>>
>> I heard that the MeanCurv is the integral of the rectified mean curvature
>> of
>> white matter surface (1/r mm), and ?h.curv is the mean curvature of the
>> white matter surface with a Gaussian smoothing kernel applied.
>> It looks that the MeanCurv and H Mean Rectified Surface Integral has only
>> positive values, while the H  and ?h.curv has positive or negative
>> value.
>>
>> I wonder whether MeanCurv and ?h.curv has the difference meaning or
>> difference formula.
>> And I would like to know the meaning of the ?h.curv negative value.
>> Is H  ( by mris_curvature_Stats ) compute from ?h.curv ?
>>
>>
>> Thank you.
>>
>> Han.
>>
>>
>>
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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Bruce Fischl]

Hi Han

I'm not sure I understand you question. The sign of the curvature depends 
on the arbirary convention you choose for the normal vector field over the 
surface. We pick and outwards pointing normal, which means that gyral 
regions in general have negative curvature (since they lie 'below' the 
tangent plane in terms of their dot product with the normal) and sulcal 
ones are positive. AFAIK both the ?h.white.H and ?h.curv curvatures obey 
this convention, although the smoothing applied to the ?h.curv will mean 
that some places they will have different sign. If you plot them both you 
will see that they are pretty highly correlated though.


Does that answer your question? If not, can you clarify?

cheers
Bruce



On Sun, 2 Oct 2016, Hanbyul Cho wrote:


Dear FreeSurfer Team,

I apologize for the repetitive questions.

I made 2 labels which included bilateral paracentral lobule and sulcus
regions.
Then I extract the values:  
   - MeanCurv
     After mris_anatomical_stats processing, I extracted the MeanCurv by the
command,  
  'aparcstats2table --hemi ?h --parc  --meas meancurv --subjects
 --tablefile '

   - ?h.Curv  
      After mris_anatomical_stats processing with the option '-t lh.curv', I
extracted the curvature value by the command,
  'aparcstats2table --hemi ?h --parc  --meas thickness--subjects
 --tablefile '

  - H  +- ,   H Mean Rectified Surface Integral
    The Mean curvature values were compute by the command,
    'mris_curvature_Stats -l  -g -n -m -f white -o 
 ?h'

I analyzed the each value. The ?h.Curv mean (within the label) has opposite
relationship with Z value compared to MeanCurv, while similar relationship
with Z value compared to H .

I heard that the MeanCurv is the integral of the rectified mean curvature of
white matter surface (1/r mm), and ?h.curv is the mean curvature of the
white matter surface with a Gaussian smoothing kernel applied.
It looks that the MeanCurv and H Mean Rectified Surface Integral has only
positive values, while the H  and ?h.curv has positive or negative
value.

I wonder whether MeanCurv and ?h.curv has the difference meaning or
difference formula.
And I would like to know the meaning of the ?h.curv negative value.
Is H  ( by mris_curvature_Stats ) compute from ?h.curv ?


Thank you.

Han.


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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear FreeSurfer Team,

I apologize for the repetitive questions.

I made 2 labels which included bilateral paracentral lobule and sulcus
regions.
Then I extract the values:
   - MeanCurv
 After mris_anatomical_stats processing, I extracted the MeanCurv by
the command,
  'aparcstats2table --hemi ?h --parc  --meas meancurv --subjects
 --tablefile '

   - ?h.Curv
  After mris_anatomical_stats processing with the option '-t lh.curv',
I extracted the curvature value by the command,
  'aparcstats2table --hemi ?h --parc  --meas thickness--subjects
 --tablefile '

  - H  +- ,   H Mean Rectified Surface Integral
The Mean curvature values were compute by the command,
'mris_curvature_Stats -l  -g -n -m -f white -o 
 ?h'

I analyzed the each value. The ?h.Curv mean (within the label) has opposite
relationship with Z value compared to MeanCurv, while similar relationship
with Z value compared to H .

I heard that the MeanCurv is the integral of the rectified mean curvature
of white matter surface (1/r mm), and ?h.curv is the mean curvature of the
white matter surface with a Gaussian smoothing kernel applied.
It looks that the MeanCurv and H Mean Rectified Surface Integral has only
positive values, while the H  and ?h.curv has positive or negative
value.

I wonder whether MeanCurv and ?h.curv has the difference meaning or
difference formula.
And I would like to know the meaning of the ?h.curv negative value.
Is H  ( by mris_curvature_Stats ) compute from ?h.curv ?


Thank you.

Han.
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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl,

Thank you for your help.

Best Regards,

Han Byul Cho

On Fri, Sep 16, 2016 at 8:27 PM, Bruce Fischl 
wrote:

> Hi Han
>
> the ?h.curv files are the mean curvature of the white matter surface with
> a Gaussian smoothing kernel applied to it over space. The ?h.curv.pial is
> the same thing for the pial surface. The ?h.inflated.H is the (unsmoothed)
> curvature of the inflated surface, and the ?h.inflated.K is the same but
> Gaussian curvature.
>
>
> cheers
> Bruce
>
>
> On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>
> Dear Bruce Fischl,
>>
>> Thank you for your explanation.
>>
>> I think I could not yet fully understand the 'curv' files.
>> After processed this command,
>> recon-all -s  -i  -all
>>
>> the output files were follow as,
>> surf/?h.curv
>> surf/?h.curv.pial
>> surf/?h.inflated.H
>> surf/?h.inflated.K
>>
>> I wonder all these output files contained 'spatially smoothed mean
>> curvature'.
>>
>> Could I know that the meaning of 'spatially smoothed' ?
>> Are these output files difference from the output of 'mris_curvature'
>> command?
>>
>>
>> I saw the values that
>> stats/?h.aparc.stats   and
>> stats/?h.aparc.a2009s.stats
>> contained the 'integrated rectified Mean curvature' and 'integrated
>> rectified Gaussian curvature'.
>>
>> I wonder these values were if the average curvature of vertices in each
>> region, or other computed values using different atlas parcellation level.
>>
>> I appreciate your help.
>>
>> Best Wishes,
>>
>> Han.
>>
>> On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl > >
>> wrote:
>>   Hi Han
>>
>>   the files ?h.curv contain the spatially smoothed mean curvature.
>>   You can compute the mean or Gaussian (or principal) curvatures
>>   of any surface using the mris_curvature command.
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>
>>   On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>>
>> Dear FreeSurfer Team,
>>
>>
>> I heard that FreeSurfer could calculate the Gaussian
>> curvature and Mean
>> curvature by vertex level.
>>
>> Do the computed curvature values be saved as the
>> subject/surf/lh.curv  or
>> rh.curv  files?
>>
>>
>> When I prepared the generated mass-univariate data,
>> I used the mris_preproc
>> with [--meas curv] option, not [--meas thickness].
>>
>> mris_preproc --qdec-long qdec.table.dat --target
>> study_average --hemi lh
>> --meas curv--out lh.curv.mgh
>>
>> I wonder this option is right usage to analyze the
>> cortical curvature. And I
>> wonder the 'curv' is what specific value is meaning.
>>
>>
>> If I want to designate the specific curvature
>> values(Gaussian or Mean
>> curvature ) to analyze by vertex level, how can I
>> use the [--meas] option?
>>
>>
>> Thank you,
>>
>> Best wishes,
>>
>> Han.
>>
>>
>>
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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.
>>
>>
>>
>>
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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Bruce Fischl]

Hi Han

the ?h.curv files are the mean curvature of the white matter surface with a 
Gaussian smoothing kernel applied to it over space. The ?h.curv.pial is the 
same thing for the pial surface. The ?h.inflated.H is the (unsmoothed) 
curvature of the inflated surface, and the ?h.inflated.K is the same but 
Gaussian curvature.


cheers
Bruce


On Fri, 
16 Sep 2016, Hanbyul Cho wrote:



Dear Bruce Fischl,

Thank you for your explanation.

I think I could not yet fully understand the 'curv' files.
After processed this command,
recon-all -s  -i  -all

the output files were follow as,
surf/?h.curv
surf/?h.curv.pial
surf/?h.inflated.H
surf/?h.inflated.K

I wonder all these output files contained 'spatially smoothed mean
curvature'.

Could I know that the meaning of 'spatially smoothed' ?
Are these output files difference from the output of 'mris_curvature'
command?


I saw the values that 
stats/?h.aparc.stats   and
stats/?h.aparc.a2009s.stats
contained the 'integrated rectified Mean curvature' and 'integrated
rectified Gaussian curvature'.

I wonder these values were if the average curvature of vertices in each
region, or other computed values using different atlas parcellation level.

I appreciate your help.

Best Wishes,

Han.

On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl 
wrote:
  Hi Han

  the files ?h.curv contain the spatially smoothed mean curvature.
  You can compute the mean or Gaussian (or principal) curvatures
  of any surface using the mris_curvature command.

  cheers
  Bruce




  On Fri, 16 Sep 2016, Hanbyul Cho wrote:

Dear FreeSurfer Team,


I heard that FreeSurfer could calculate the Gaussian
curvature and Mean
curvature by vertex level.

Do the computed curvature values be saved as the
subject/surf/lh.curv  or
rh.curv  files?


When I prepared the generated mass-univariate data,
I used the mris_preproc
with [--meas curv] option, not [--meas thickness].

mris_preproc --qdec-long qdec.table.dat --target
study_average --hemi lh
--meas curv--out lh.curv.mgh

I wonder this option is right usage to analyze the
cortical curvature. And I
wonder the 'curv' is what specific value is meaning.


If I want to designate the specific curvature
values(Gaussian or Mean
curvature ) to analyze by vertex level, how can I
use the [--meas] option?


Thank you,

Best wishes,

Han.



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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl,

Thank you for your explanation.

I think I could not yet fully understand the 'curv' files.

After processed this command,
recon-all -s  -i  -all

the output files were follow as,
surf/?h.curv
surf/?h.curv.pial
surf/?h.inflated.H
surf/?h.inflated.K

I wonder all these output files contained 'spatially smoothed mean
curvature'.

Could I know that the meaning of 'spatially smoothed' ?
Are these output files difference from the output of 'mris_curvature'
command?


I saw the values that
stats/?h.aparc.stats   and
stats/?h.aparc.a2009s.stats
contained the 'integrated rectified Mean curvature' and 'integrated
rectified Gaussian curvature'.

I wonder these values were if the average curvature of vertices in each
region, or other computed values using different atlas parcellation level.

I appreciate your help.

Best Wishes,

Han.

On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl 
wrote:

> Hi Han
>
> the files ?h.curv contain the spatially smoothed mean curvature. You can
> compute the mean or Gaussian (or principal) curvatures of any surface using
> the mris_curvature command.
>
> cheers
> Bruce
>
>
>
>
>
> On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>
> Dear FreeSurfer Team,
>>
>>
>> I heard that FreeSurfer could calculate the Gaussian curvature and Mean
>> curvature by vertex level.
>>
>> Do the computed curvature values be saved as the subject/surf/lh.curv  or
>> rh.curv  files?
>>
>>
>> When I prepared the generated mass-univariate data, I used the
>> mris_preproc
>> with [--meas curv] option, not [--meas thickness].
>>
>> mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh
>> --meas curv--out lh.curv.mgh
>>
>> I wonder this option is right usage to analyze the cortical curvature.
>> And I
>> wonder the 'curv' is what specific value is meaning.
>>
>>
>> If I want to designate the specific curvature values(Gaussian or Mean
>> curvature ) to analyze by vertex level, how can I use the [--meas] option?
>>
>>
>> Thank you,
>>
>> Best wishes,
>>
>> Han.
>>
>>
>>
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Re: [Freesurfer] Gaussian curvature or Mean curvature

[Bruce Fischl]

Hi Han

the files ?h.curv contain the spatially smoothed mean curvature. You can 
compute the mean or Gaussian (or principal) curvatures of any surface 
using the mris_curvature command.


cheers
Bruce




On Fri, 16 Sep 2016, Hanbyul Cho wrote:


Dear FreeSurfer Team,


I heard that FreeSurfer could calculate the Gaussian curvature and Mean
curvature by vertex level.

Do the computed curvature values be saved as the subject/surf/lh.curv  or
rh.curv  files?


When I prepared the generated mass-univariate data, I used the mris_preproc
with [--meas curv] option, not [--meas thickness].

mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh
--meas curv--out lh.curv.mgh

I wonder this option is right usage to analyze the cortical curvature. And I
wonder the 'curv' is what specific value is meaning.


If I want to designate the specific curvature values(Gaussian or Mean
curvature ) to analyze by vertex level, how can I use the [--meas] option?


Thank you,

Best wishes,

Han.


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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
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