[Freesurfer] area and smoothing
Dear Freesurfer experts, 1. I want to compare the area and/or areapial between two groups in qdec menu. I think that the eTIV or total surface area should be used as a covariate. Which is more appropriate between eTIV and total surface area? 2. Is there any guideline or rule for the smoothing in the thickness, area, and volume comparison? How about the smoothing=5? Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ᐧ ___ 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.
Re: [Freesurfer] area and smoothing
Hi Seung-Gul, Please see below: On 16 September 2016 at 00:52, Seung Gul Kang wrote: > Dear Freesurfer experts, > > 1. I want to compare the area and/or areapial between two groups in qdec > menu. > I think that the eTIV or total surface area should be used as a covariate. > Which is more appropriate between eTIV and total surface area? > Using and not using a global measurement tell each different things, and a suggestion (I'd say a recommendation) is to run both ways, i.e., with and without global area as nuisance, and use the results from both when reading and interpreting the findings. Regarding ICV, it has substantial correlation with area and it can be included as nuisance in the same model in which global area is included. It is not a problem that they are correlated as both go as nuisance in the group comparison. > > 2. Is there any guideline or rule for the smoothing in the thickness, > area, and volume comparison? > How about the smoothing=5? > There is no specific rule. We have investigated with as little as 10 mm on the sphere and the results of the default area processing in FS become virtually indistinguishable from the exact method that we proposed in 2012. Although we did not investigate 5mm, we did look also into the ic5 and ic3 resolutions and, particularly for the ic5 (that has vertices about 4 times farther from each other compared to the default ic7), 10 mm smoothing is fine, suggesting that 5 mm would likewise lead to similar results for the ic7. A summary of these findings is in a manuscript that we have just uploaded to bioRxiv: http://dx.doi.org/10.1101/074666 (for this particular question the SI is probably more important). All the best, Anderson > > Thank you. > > Best, > Seung-Gul > > --- > *Seung Gul Kang, M.D., Ph.D. * > > *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil > Medical Center, Gachon University, School of Medicine, 21, Namdong-daero > 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > *Research scholar*; Sleep Disorders Clinical Research Program, Department > of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 > Bowdoin Square, 9th floor, Boston, MA 02114, USA > *Collaboration researcher*; Division of Sleep & Circadian Disorders, > Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, > Boston MA 02115 > ᐧ > > ___ > 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.
Re: [Freesurfer] area and smoothing
Hi Anderson, Thank you so much for your answer. I really appreciate it. All the Best, Seung-Gul ᐧ --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 2016-09-17 3:26 GMT-04:00 Anderson M. Winkler : > Hi Seung-Gul, > > Please see below: > > On 16 September 2016 at 00:52, Seung Gul Kang > wrote: > >> Dear Freesurfer experts, >> >> 1. I want to compare the area and/or areapial between two groups in qdec >> menu. >> I think that the eTIV or total surface area should be used as a covariate. >> Which is more appropriate between eTIV and total surface area? >> > > Using and not using a global measurement tell each different things, and a > suggestion (I'd say a recommendation) is to run both ways, i.e., with and > without global area as nuisance, and use the results from both when reading > and interpreting the findings. > > Regarding ICV, it has substantial correlation with area and it can be > included as nuisance in the same model in which global area is included. It > is not a problem that they are correlated as both go as nuisance in the > group comparison. > > > >> >> 2. Is there any guideline or rule for the smoothing in the thickness, >> area, and volume comparison? >> How about the smoothing=5? >> > > There is no specific rule. We have investigated with as little as 10 mm on > the sphere and the results of the default area processing in FS become > virtually indistinguishable from the exact method that we proposed in 2012. > Although we did not investigate 5mm, we did look also into the ic5 and ic3 > resolutions and, particularly for the ic5 (that has vertices about 4 times > farther from each other compared to the default ic7), 10 mm smoothing is > fine, suggesting that 5 mm would likewise lead to similar results for the > ic7. A summary of these findings is in a manuscript that we have just > uploaded to bioRxiv: http://dx.doi.org/10.1101/074666 (for this > particular question the SI is probably more important). > > All the best, > > Anderson > > > > >> >> Thank you. >> >> Best, >> Seung-Gul >> >> --- >> *Seung Gul Kang, M.D., Ph.D. * >> >> *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil >> Medical Center, Gachon University, School of Medicine, 21, Namdong-daero >> 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea >> *Research scholar*; Sleep Disorders Clinical Research Program, >> Department of Psychiatry, Massachusetts General Hospital, Harvard Medical >> School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA >> *Collaboration researcher*; Division of Sleep & Circadian Disorders, >> Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, >> Boston MA 02115 >> ᐧ >> >> ___ >> 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. > > ___ 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 t
