Hi Ellen The folding index is pretty sensitive to kmax, which can be huge for tiny antennae and such. It may not be the right measure for what you are trying to capture. You can always compute the curvatures with mris_curvature then overlay them and see if there are outlier values, or find the max in matlab or something, but in the end you may want to quantify things differently.

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Monday, April 19, 2021 9:06 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Abormally high foldind index

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Hi Bruce,

I looked at the pial surfaces and WM by running this for the outlier subjects:

freeview -v subject1/mri/T1.mgz \ subject1/mri/brainmask.mgz \ -f subject1/surf/lh.white:edgecolor=yellow \ subject1/surf/lh.pial:edgecolor=red \ subject1/surf/rh.white:edgecolor=yellow \ subject1/surf/rh.pial:edgecolor=red

Nothing stood out to me. Is there anything else you suggest I investigate? What could explain a negative folding index?

Best, Ellen

On 3/31/2021 12:18 AM, Fischl, Bruce wrote:

Hi Ellen

It is certainly possible. Have you looked at the surfaces for those subjects?

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Tuesday, March 30, 2021 5:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Abormally high foldind index

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Dear Experts,

While the majority of our subjects have a folding index between 5-30, there are a couple of *extreme* outliers in the thousands or even negative.

Could this hint that a particular part of recon-all failed and should be rerun?

Thank you for your interpretation and advice!

-Ellen

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