Hi Bruce,

Thanks for your email. We are actually interested in looking at k though and I was wondering what surfaces you use for the numerator and denominator.

Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

I think mris_jacobian computes and applies the scale factor for you. The group average surface area is the average surface area of the individuals that went into the group, since the average subject has less surface area than any of the individuals. Doug uses this to compute the proper cluster sizes, but it shouldn't matter for the jacobian analysis.

cheers, Bruce

On Tue, 26 Jun 2007, Morgan Hough wrote:

...

Hi there,

I would like to ask some questions about metric distortion.

1. Following the Wisco et al (2007) paper, metric distortion is

defined as

Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white interface surface

which I believe I can compute using

mris_jacobian $subject/surf/lh.sphere $subject/surf/lh.sphere.reg $subject/surf/lh.sphere.reg.jacobian

The subject 's ?h.sphere.reg is formed from the registration of the inflated sphere of the subject with the Desikan et al. (2006) 40 subject template? From the wiki, I think the command is

mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg

so the jacobian measure is derived from the parcellation stage (stage3) of recon-all.

2. I would like to extract the k factor for each subject which is

defined as

k = total surface area of original gray/white interface surface / total surface area of individual sphere

do I compute this from the total surface area field of

mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats $subject $hemi sphere

or do I need to use outputs from different surfaces or extract either value differently? The sphere values look rather uniform and I wanted to check if I am using the right thing.

3. Finally, I see in the study average make_average_surface.log file:

setting group surface area to be 1142.0 cm^2 (scale=1.29)

and I was wondering what the scale factor represented here.

Thanks in advance for your time.

Cheers,

-Morgan

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Thanks - so how do we get k! Cheers.

On 26 Jun 2007, at 18:27, Bruce Fischl wrote:

Hi Morgan,

you specify the original surface you want to use, but typically we use the ?h.white.

Bruce On Tue, 26 Jun 2007, Morgan Hough wrote:

...

Hi Bruce,

Thanks for your email. We are actually interested in looking at k though and I was wondering what surfaces you use for the numerator and denominator.

Cheers,

-Morgan

Bruce Fischl wrote:

...

Hi Morgan, I think mris_jacobian computes and applies the scale factor for you. The group average surface area is the average surface area of the individuals that went into the group, since the average subject has less surface area than any of the individuals. Doug uses this to compute the proper cluster sizes, but it shouldn't matter for the jacobian analysis. cheers, Bruce On Tue, 26 Jun 2007, Morgan Hough wrote:

...

Hi there, I would like to ask some questions about metric distortion.

1. Following the Wisco et al (2007) paper, metric distortion is

defined as Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white interface surface which I believe I can compute using mris_jacobian $subject/surf/lh.sphere $subject/surf/ lh.sphere.reg $subject/surf/lh.sphere.reg.jacobian The subject 's ?h.sphere.reg is formed from the registration of the inflated sphere of the subject with the Desikan et al. (2006) 40 subject template? From the wiki, I think the command is mris_register -curv ?h.sphere $FREESURFER_HOME/average/? h.average.curvature.filled.buckner40.tif ?h.sphere.reg so the jacobian measure is derived from the parcellation stage (stage3) of recon-all. 2. I would like to extract the k factor for each subject which is defined as k = total surface area of original gray/white interface surface / total surface area of individual sphere do I compute this from the total surface area field of mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats $subject $hemi sphere or do I need to use outputs from different surfaces or extract either value differently? The sphere values look rather uniform and I wanted to check if I am using the right thing. 3. Finally, I see in the study average make_average_surface.log file: setting group surface area to be 1142.0 cm^2 (scale=1.29) and I was wondering what the scale factor represented here. Thanks in advance for your time. Cheers, -Morgan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---