Re: [Freesurfer] Abormally high foldind index
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-boun...@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 External Email - Use Caution 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-boun...@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 > > External Email - Use Caution > > 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 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc6 > 9QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1 > rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXV > wC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wW > sn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc6 > 9QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1 > rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXV > wC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wW > sn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Abormally high foldind index
External Email - Use Caution 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-boun...@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 > > External Email - Use Caution > > 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 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc69QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXVwC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wWsn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc69QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXVwC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wWsn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Abormally high foldind index
Hi Ellen It is certainly possible. Have you looked at the surfaces for those subjects? Cheers Bruce -Original Message- From: freesurfer-boun...@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 External Email - Use Caution 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Abormally high foldind index
External Email - Use Caution 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
