External Email - Use Caution Dear Thomas and FreeSurfer experts,
Here I am just reposting my question below - just in case this was missed by the experts. Any help would be really appreciated. ---------- Forwarded message --------- From: Martin Juneja <mj70...@gmail.com> Date: Sat, Jul 10, 2021 at 3:45 PM Subject: Re: [Freesurfer] Fwd: Yeo atlas for children! To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Dear Thomas, Thanks for your response. I have one more question here: I was looking at the Schaefer parcellation paper where authors have 100, 200, 300, 500...1000 areas parcellation. Is there a way to choose among these parcellations (i.e., what's the basic difference/justification/significance of each of these parcellations over one another) for cortical structure analysis? Thanks! On Thu, Jun 24, 2021 at 7:24 PM Thomas Yeo <ytho...@csail.mit.edu> wrote: > External Email - Use Caution > > Hi Martin, > > With regards to adolescents versus adults, there's obviously differences > between the two age groups. In our experience, when we re-estimate > parcellations from this study (*MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1imRwMSixADMoOIgpdpY29jXpDOLeSGli2a22XCxZWFbr2XZcnxO2KDrRbNMcsCgQMkiZ1MsPEXG3o-3E9Y8PqOAA_WXMSVytHVXo0IghuduA56nI9K7IG2cxiGQ_6nU-TWPhPW-etqRzG5uQOkyA64SXMxYawNeZNm5ggMchWgpwYLmUPctZnCmo5pQTBNUxJVA-pQ6-EihauZbmWBsHMIqTlPg1U5vnpftP9B9whY1fRvPAL2YtklY-zX6zcEdUx_jAncDqCVT0lDpZ1ciI5A/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101 > <https://secure-web.cisco.com/1TF7OmC5fKijUUx5uZkr1n5IUfkGr1RFX7MO-EmdsI3fo1_9zP0Jp-ETRw5NAjxS8BJDa6kKcSMMpJ2sdiX-ot-j-5QFedPJw2Pv_w_Lx09S2qip068nmS_qYJ7jPemY60cjnwP8Sv5YsnioL9TmWNC25owkxNqJp4Z23siRPlxWMF6odSKRD90PbJNM9pQK60dgMUgk07qeKbxs2PfIzD7evz-QcmOcS6NgyV6QttV9sTK7p2YtU6VOPRTXrkqV29tPjdaVkUQg-0QMGTS-45w/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101>) > in kids (ABCD), the parcellations are not better based on various metrics > we computed, so I suspect it won't matter much. But the kids results are > not in our paper, so I am not sure the reviewer will buy this argument. For > this issue, you could reapply the Yeo2011 algorithm (*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to > be* > https://secure-web.cisco.com/1TRaCda3Ajq2cSPkyOdjhs-iDjMQqQpE0pfWxMyCDpAO5VRbGYtKOT3ESGeNIkcwZ3mCdJhReWuzhWi9pXY1grfJSeKsSmO-OkwTvwN9ji0-lW8jAdGenRsKwBA7v5mgvFY_fzJo8AWJ223pcmruUzdI5R-Dhb-eLfDUtqAxn0Ck8lp3PhZmPBc27-snFbAikXbe9ZlzLVPdJyPmXQyvKeo3GhIDUbbE9J8uq_cgSgK727TvQLtqTArCX1ZPbDFIMNadY2RHLMtyxLZJf2OoiWA/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering > <https://secure-web.cisco.com/1Z2srwkLUjJ_Dnco-Ccq_78ppkQhV3eTVmdR3bkvuvg64MLymHCpblVH7s3BbaYqCgmBhjfn2fLmvOxE52eTv_pNlqqJU66mrQ_kyS9r5xo7vnpF49mnl1CurnSQ-g0lBHQrOu-r1VaMu4bdeod4wOunBUn8z0Ilju3bxxxEVIBwddrah-4RY6d0MV-0qlYnFyxyw5vpq66r2twE7Xzv--mIsL85psoPahHst1Vto9_q39hxhT94w3fNtgOpITnrC9jSZStJGUBEPMuLDb7fWgQ/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering>) > to your sample and estimate cohort-specific networks and repeat your > analysis. We have also developed individual-specific versions of the > Yeo2011 networks (*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1uqONT3oR5bPf0SnEdMW-1CdNAMyYxLbz75N5HGX7ryuRL5BtKUre5JkOu_xWBiMu_7SE5xf0aYHXK_YbkZORrCStIQKqz9-pVg38BsiqqAP1ovmM-smi2l9ELT95KkAE9W1ErC0eDnRQvCYR4aoatuT2EfPobOkfxk7-TDdW-xaWuZiaBdZBA2Qs39dCKia-pDrE92rVfPquYg8jm1JhOhfxFPmV4NBmIvCpuOwb8hrzFDfWKd5LB_n4hn3CQRo4WkRwVaaaUPg5hSnPJe0AZw/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM > <https://secure-web.cisco.com/1ja6ZcGwaTlynHGpv68CpBe5wYiryA6Cd9PoPXavhiQcOfiz9Dqk182Jm1NOGknuS5V4LN5APd8rzUErhPpJ6N8fmbPbU1ofhucuPYirEkxbiN-f7KwiyDUiW26HQYY_APS_F3PptKP35VM14zsTm7TwwBSzRZcp1x2GUabhSkC2Uwedw4JQXh_Wned1PegQitYecAZLY0yG_RxpEISUp9zo-MvBV5DdGwVNYsVx8cRr1imnAjiZgQ241c3ZHSKJsuA3WlEi0QZmaYA9NYNL2Ng/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM>), > which you might find helpful, although it's probably not necessary based on > the reviewer's comments. > > The other issue is whether a functional atlas might be appropriate for > structural data. I think that really depends on your question. For example, > if your question is whether default network cortical thickness might be > different between adolescents and adults, I think it's reasonable to use a > functional atlas where the default network is well defined. If you use a > structural atlas like the Desikan-Kiliany atlas, then you will still need > to use a functional atlas to roughly assign the Desikan-Kiliany parcels to > the default network, which does not seem that great either. > > Regards, > Thomas > > On Fri, Jun 25, 2021 at 12:52 AM Martin Juneja <mj70...@gmail.com> wrote: > >> External Email - Use Caution >> >> >> Hi all, >> >> I am reposting my concerns below. I would really appreciate any help. >> >> ---------- Forwarded message --------- >> From: Martin Juneja <mj70...@gmail.com> >> Date: Fri, Jun 18, 2021 at 6:16 PM >> Subject: Yeo atlas for children! >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> >> >> Dear experts, >> >> I used Yeo's 17-network parcellation to study the association between >> network-wise cortical volume and a clinical variable in adolescents. I >> received the following two questions from the reviewers regarding the use >> of Yeo's atlas. I would really appreciate if someone could help us in >> addressing these questions: >> >> >> >> *1) Could the author justify their choice to use a functional >> parcellation on structural data? How is using this parcellation helpful in >> understanding the brain? All in all, the authors need to justify the >> superiority of using Yeo's 17-area parcellations on structural data over >> other methods of parcellation/analysis. * >> *2) One issue with Yeo's parcellation also stems from the fact that this >> parcellation was derived from adult connectomes. Could the authors also >> address this issue and provide examples that justify their approach.* >> >> Thanks. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1KRwXT4VwQBvO8caiW-w8jMeWvvE3KMx_nAH0pD5t6Gm76pjtZsFQ7mVz50cBn_onsIIpqooTZTgBuX29wLS4xJ8VK9oIzWXxHZFCEePmD3HnqlnzwZ7Ddial4JRj66MnosTZDZSaq4otjCBhYwIjBu_kZfEUErNPJneRiutevK4DsGm_a8Q09gKzmNFIfY3QGosvJb0YIsPe-OZoaDwIq2q0zxeWPkksT6dzTfNvqJ-cRfJ4aE-pDs1lskIDG2WihT-jsgppb_eH-sSDP6NwcQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1vYwj4u8tnnloAFkq4GNee0aO8bp4AJUBz-f6_rsP7s37_gWii9gsMI3T4i80MIoKCmaAbgSDavMI9Bra-Qk7FqwHAR__FBeRuuC3XCpet50brzAn5-A8K5-0JOTdZXjrfA1qCqFs04yCTLQy1mTe7wOXzmWFuHfI7dyoNfQpgcuJM0neywH2WO4quKfZx9e2C_pm4ronht7RD98Axtw5iLCfeiE4ofV57OGHobrbOveEjP3csgYMC7ZS_59V7Kxia-b8F9Ct_3ip4R_Lpq0PyA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1KRwXT4VwQBvO8caiW-w8jMeWvvE3KMx_nAH0pD5t6Gm76pjtZsFQ7mVz50cBn_onsIIpqooTZTgBuX29wLS4xJ8VK9oIzWXxHZFCEePmD3HnqlnzwZ7Ddial4JRj66MnosTZDZSaq4otjCBhYwIjBu_kZfEUErNPJneRiutevK4DsGm_a8Q09gKzmNFIfY3QGosvJb0YIsPe-OZoaDwIq2q0zxeWPkksT6dzTfNvqJ-cRfJ4aE-pDs1lskIDG2WihT-jsgppb_eH-sSDP6NwcQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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