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.
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.
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 <subject> -i <input file> -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 fischl@nmr.mgh.harvard.edu 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 <subject> -i <input file> -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 fischl@nmr.mgh.harvard.edu 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce Fischl,
Thank you for your help.
Best Regards,
Han Byul Cho
On Fri, Sep 16, 2016 at 8:27 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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 <subject> -i <input file> -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 <fischl@nmr.mgh.harvard.edu
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 <label> --meas meancurv --subjects <subjects list> --tablefile <output.txt>'
- ?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 <label> --meas thickness--subjects <subjects list> --tablefile <output.txt>'
- H <mean> +- <std>, H Mean Rectified Surface Integral The Mean curvature values were compute by the command, 'mris_curvature_Stats -l <label> -g -n -m -f white -o <output.txt> <subject> ?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 <mean>.
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 <mean> 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 <mean> ( by mris_curvature_Stats ) compute from ?h.curv ?
Thank you.
Han.
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 <label> --meas meancurv --subjects <subjects list> --tablefile <output.txt>'
- ?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 <label> --meas thickness--subjects <subjects list> --tablefile <output.txt>'
- H <mean> +- <std>, H Mean Rectified Surface Integral The Mean curvature values were compute by the command, 'mris_curvature_Stats -l <label> -g -n -m -f white -o <output.txt> <subject> ?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 <mean>.
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 <mean> 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 <mean> ( by mris_curvature_Stats ) compute from ?h.curv ?
Thank you.
Han.
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 fischl@nmr.mgh.harvard.edu 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 <label> --meas meancurv --subjects <subjects list> --tablefile <output.txt>'
- ?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 <label> --meas thickness--subjects <subjects list> --tablefile <output.txt>'
- H <mean> +- <std>, H Mean Rectified Surface Integral The Mean curvature values were compute by the command, 'mris_curvature_Stats -l <label> -g -n -m -f white -o <output.txt>
<subject> ?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 <mean>.
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 <mean> 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 <mean> ( by mris_curvature_Stats ) compute from ?h.curv ?
Thank you.
Han.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 fischl@nmr.mgh.harvard.edu 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 <label> --meas meancurv --subjects <subjects list> --tablefile <output.txt>' - ?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 <label> --meas thickness--subjects <subjects list> --tablefile <output.txt>' - H <mean> +- <std>, H Mean Rectified Surface Integral The Mean curvature values were compute by the command, 'mris_curvature_Stats -l <label> -g -n -m -f white -o <output.txt> <subject> ?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 <mean>. 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 <mean> 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 <mean> ( by mris_curvature_Stats ) compute from ?h.curv ? Thank you. Han.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Bruce Fischl
I appreciate your explanation. Thank you.
Best Wishes,
Han
On Mon, Oct 3, 2016 at 11:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu 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 <label> --meas meancurv --subjects <subjects list> --tablefile <output.txt>' - ?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 <label> --meas thickness--subjects <subjects list> --tablefile <output.txt>' - H <mean> +- <std>, H Mean Rectified Surface Integral The Mean curvature values were compute by the command, 'mris_curvature_Stats -l <label> -g -n -m -f white -o <output.txt> <subject> ?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 <mean>. 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 <mean> 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 <mean> ( by mris_curvature_Stats ) compute from ?h.curv ? Thank you. 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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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Hanbyul Cho