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Dear Dr. Greve,
I trust this message finds you well. I wanted to follow up on the inquiry I posted to the FreeSurfer mailing list a while back regarding "About Mean LGI value" as below. I understand you are busy, and I appreciate your dedication to the community. If possible, could you revisit my query when time permits? Thank you for your time, and I look forward to hearing from you.
Best, Daiki Sasabayashi
転送されたメッセージ:
差出人: 笹林大樹 <ds179@med.u-toyama.ac.jp mailto:ds179@med.u-toyama.ac.jp> 件名: Re: [Freesurfer] About Mean LGI value 日付: 2023年11月9日 10:37:38 GMT-5 宛先: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> 返信先: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
External Email - Use CautionDear. Dr. Greve,
Thank you for your response. I attached both “*h.aparc.pial_lgi.stats” and “*h.aparc.mean_pial_lgi.stats” files. For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, Seg0001, is it correct as mean LGI value?), while the average of the LGI values is about 3.0327 (the sum of the LGI values of the 34 DK atlas ROIs divided by 34: value calculated here). Are these values acceptable?
Daiki Sasabayashi
2023/11/09 9:33、Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU>のメール:
How different are the values? Those two stats files are created with different programs, so there could be some small differences. But if you're seeing large differences, then that is something else. If the latter, then send both stats files.
On 11/3/2023 9:14 AM, 笹林大樹 wrote:
External Email - Use CautionDear Freesurfer experts,
I have calculated the mean LGI value for each hemisphere by referring to previous archives below. However, this mean LGI value differs from the average of the LGI values listed in *h/aparc.pial_lgi.stats (i.e., the sum of the LGI values of the 34 DK atlas ROIs divided by 34). Are these values originally subject to discrepancy?
Best,
Daiki Sasabayashi
Re: [Freesurfer] Mean Gyrification index https://secure-web.cisco.com/1EEmYXs8gGLqnLaQO_vg2nJ_Fvpf2fzioffwk6p2gnV2-Z9JdzqI4XaiyIk1SS6IVvttJatU3Yej90oVOG214tzWZoRvuA7-nw-2yADK-BUEYczlH05OczaRnN5SMBHJDgteAxO4UbTjdykBGnTk9Snv_O28tND-rWD8lrpy8Kz-ohRZRPOhbwnzAW0N1mJxF65GKOb6fzCzvEBOJ31DOOTZBHF83dMXfe5Iw7GICai8479G8Ps3bpjLwN62IL4zzj749-L2Og7_8h9GHnUpAp08q-rt9lJrl6daOBxtPZwakqxfgh86ZiThHwhjAAHsj/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522Re%255C%253A%2B%255C%255BFreesurfer%255C%255D%2BMean%2BGyrification%2Bindex%2522%26o%3Dnewest Dougla s N. Greve https://secure-web.cisco.com/155etTRjlbOK03N6VnyYbCi9rjZvuuTH6VS0qZwFyCNvBCgiZuQfPzA6ucEmisq0DRJzR_9C8WhRa770AHQsT9Qj0I1UbSYfvdn1BeUemV9fuLvDPa0kOQjjYaNbrXpidach13O5sCgS_6rgPmSCDtoaW956QhLdQwcWP4NG9l8BQsytrlZz3-sdOd-6IvjnNOk9PHV7Cguz81T1SZ_ph7tJx0Vmn-C12aby1dVnRtAgopnajhq8QONH8qveQSsEYsA0UU9LeCtHW9pTzm4DPsH4cx7Yc58CpX6sPwkCyJYnNbk72jcW_Vp2b6kw-pwF9/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522 Wed, 09 Sep 2020 08:26:32 -0700 https://secure-web.cisco.com/1M3mEVNkqqL6k6z2gdfeh6rZadzY9YD3LDHndCtPD568i5z5wTvu5gT5a_EY2u7PWqAHyr-anuwvbVDRQvmFMVDUn7XorKhOJ5QzjjSv0UYNSqkW7fP3T2w8nzb-0IqhioZ4uT6X5gMeU5SlZI11xwfN4qER0HfkHh-AMKLyx_54Sxs44naDXIfsrav_QyvM8f2FmvaKEt7kbhaf9h_IP177gduPUXPNeZkXQSjDctWR34IkDkY0iqzh9s_5DUy3OLXIHxUnZCIqK84KmKMa0r59bKWObvexIoAgSh-rwzEK2d44jm0knqw5F7m9OgVRu/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20200909 It is giving you values for two segmentations: inside the label and outside the label. Use --id 1 to get only values inside the cortex label On 9/9/2020 11:27 AM, vittal korann wrote: External Email - Use Caution
Dear FreeSurfer experts
I am working on the gyrification index of schizophrenia patients. I had collated global brain values such as thickness, GM, and WM volumes. In addition, I wanted to tabulate gyrification values. Using the below link I was able to extract the hemispheric mean gyrification values. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rzE1QTMGHNEaa-Oc9P0-AY3VwfCbR23FTC3O7YcjiHoF0o... https://secure-web.cisco.com/1XEfOrvgDwm2ivmcxJZotbNUpaeDPYzXRGyLreghU2caPdGgVbzNDj3P8DMShBOB_XdoKS_jPnXCfNz-xy565q6rOk4hZLktExa0VtKGBNNq_4Xxig_lw8tGj4T8f3LVEwWd3jrk9IMgG4ZR7PKIn4-96wiJ0tQYNPPrtUJZkx83b3yEveZaKB0qViVe_qUvL0W9resQjE2tWD8XJMDY5iY9X0AV97FteqTUhqzukiEfdiy5UFierIedkMj8TTKxfBO8uqGZZpDPVT9i64aHvuJ5iluz6C5Gabyuw6QlHEeKey2ic24qEKSxFnA6hrmen/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg31829.html
But it is giving me 2 rows of output that are adding more ambiguity to the existing problem. Below is the command which I used to get mean gyrification for the left hemisphere and also the corresponding output. *Command Line: *
mri_segstats --slabel CSRI104 lh /usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i /usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sumlh.aparc.pial_lgi.stats *Output: *
# NRows 2 # NTableCols 10 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 6879 4687.8 Seg0000 2.4509 0.2838 1.8067 2.8873 1.0806 2 1 128054 84259.7 Seg0001 3.0148 0.63661.9369 4.7611 2.8242 My confusion is that which row I should take it as a mean gyrification value for the left hemisphere (seg0000 or seg0001)?Please guide me if there is a way to combine two hemispheric values and make it as mean gyrification alike mean thickness. With regards Korann
On Wed, Sep 9, 2020 at 4:51 PM vittal korann <vittalkor...@MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be gmail.com http://secure-web.cisco.com/1jKyfRxer8sP76m47RQabLJ8Ic5hn5aJPCNademzz3R3mHSA-4AHSQnL82i1X9yK76JzIR9WBb7h8tfmutumrzW7OZebTEv6U9drikfhQ5NNqVVW_TeIhikXDbc-JADZZRTCF9l-8k3ThJdPmISKMYVzFOgMz0M47Kea_6D7MRLq0w-1mktSScsb1Y7TsU9sgiwTmOeN0tf8YiK0Mbj_aJmx9RftA6e9hDEeCTWzxFrQ2BBZ6c_oY7WIgL0S8f2_RdC96MEmbx5SGt6DrLXoCNJ8cjLI9Uu471wTB7BeuyK7OySPOpuJQ7yDNR2_uKTig/http%3A%2F%2Fgmail.com <mailto:vittalkor...@gmail.com mailto:vittalkor...@gmail.com>> wrote: FreeSurfer experts
I am trying to extract the mean gyrification values for the whole brain alike cortical thickness. We have all the whole-brain parameters in 'aparc.stats' file. But we do not have one for the gyrification index. Is there a way to do it? Would be grateful for your help. Best Korann */ /*
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Greve [Freesurfer] mean gyrification index https://secure-web.cisco.com/1Iuq6cDBJyOsqPW-k6wh_GIOZpVHtzqfkcjcZmG3wtLoo04H7X1is8McihrSaezxtBxQgzipqwAuiN-XFq_TJyBuB4ZPNkV887portfwgyLUZQtjQtFpY5sWIwwpYKV4Yz5LqrynYzX1xgnTCjjtr5U0Mj1brjtbA2psbV6gaFlYqzjpgxd5qbt9fNGWZtX3tjhBpQtOwhsTJICor9_9aBE5ZYFj7xbJL-RFjUrG7MlU3O6zVuszGnGWRvcJTJb9uRfFVp-RaQ5VviZEPUJJlYrLlfZIfuK910gBhP9x1l6fcrBOsxmxnTwqPjgm23x7l/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67627.html vittal korann Re: [Freesurfer] mean gyrification index https://secure-web.cisco.com/13FS3Lpb7ruVKgfwYDEZZ2Qr8QRdTXi_ilvo5Pv30_-rblEbUAwUzru0ghXUjcuMQShy507Oy_6ig5i75-tZSGWnLa14znkSZxSczFmvO4pyIxajT2UDFuu552qULiQv2N8H3AziJPp440uGGRDqZsNSTvzsTWil-0uf9AXpNYwhL5UJ-Lb0rKx89pgudhC3Ual6OgqEKQkj9oX4BzUgMHsHNDR7fBfsInAP21hLGMZkhDFhyCE_9MGm6oNwv2xrUzGT4p-AEgX1uZTQXaJR5hyvslkyCd6qLOK8rNC2k3x5SRIDGEqbe-nNMkTYRxVSS/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67628.html Douglas N. Greve Re: [Freesurfer] mean gyrification ind... https://secure-web.cisco.com/1iQ62pnYyPx33OMQwS7goUcgEX1T1vQvFyE0Kt_dL4KSJbWorfcV5O8mM5sAT2CLVTOvt3eLK9HV-hAZpbPjP607WJn6ERsbOossDcGmDgP97TiSdETPDX8GZFr6bbK0LqXG_lvxG8XGSaeBhFDv_sjAN7aFwahzjhCuk76zSzn3xI2uhbU7GNxVvTEehebNp6fq9HfVyid1e8prnaNK8svLdGcOZOl8EEeNbIOGNeDCtZsX9OG5j71DBUw_qD1ElefOjfdA1423ybRuRyFaNxEekIhMMvHalL350veTMNWv2QnsVAAmq40oOKZl4emJe/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67629.html Alexopoulos, Dimitrios Re: [Freesurfer] mean gyrification... https://secure-web.cisco.com/1cdypT1X8UYl0FvjMI2JmRQDdJomd_X45C-q5sFncgleNLlxXtbaVPJLqAGBtpUrVtbl0eQ-1NtqjOAhWktLzHp0LOdMHnMuzHAcALxZHqGKhn8vQ6pGF6pZ_-qyWy0crM1EfRtk783V6hWHbyxAZgUVEPULTvyrwuu8_UFa3uR_RFllQaeTPQLdUipxaDq4PsRuAQ9YElWSPlWF85nfrQXeYbBxpHtT6dTX4OqwDj6hQCRMNKyhU4e4AduriTpn4257CwNcBb4HO9CXTjk2a6MFHXGFayAORhKcVkjy4RR5TjGVUhAW-K60Rlw4sI1Jc/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67630.html Douglas N. Greve Re: [Freesurfer] mean gyrific... https://secure-web.cisco.com/11ll2GSLSlPDzXA-f4QvOmxl8njwtT_a-ImcVTi7cOMcOITgUP8s5E1I5SZNathFz9rvzRkfO5EoaX-SCBeD2pLD4ZkQzTn-l2yquvEJnGL2KFGG73dQb52L9FO86Lk8gn_PEGeXmtUuJKq31YNybEzL1nySmhV3qLZW9Y4jbj4HMVzv1HoJfnQMw_DctbTipDtJNzFDB5UJcg1umPxIptbMyYMcqFEW6tnu6Tq70hHGZqsQQG7X7X48q3AYsREJQfDAlVCvt09NDYhmnr4jmuv0_FQMUNdFlVP1YEQZFXS66jPaR7xxb8RJqoD0lLQi1/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67631.html Alexopoulos, Dimitrios Re: [Freesurfer] mean gyrification ind... https://secure-web.cisco.com/1KcLvrp41rV4fo-1R-8iez1bSjUKJsZE2cyQjZ7uzvBM6Y15FiOTnqxd8_sD8GkOwxXxasW_DZvQy4NGsdZnjO06rTdt73WwF2p_VraHk0SHbmVCWOyCbUPVJiAcq2FtQu_MSaveWG_-GjQT23Ih51ioSEkP4pS6lv7-cqfRKwX6Qeuy2-RHBzFgsTJG28nKtXn-y8NJIzb-JWt35lmrjbpwUIDnK5wmXYj5kcbtKg9JV1DQ_rQRbVVGyWjhRQ68sj4cYJDnbKHrTocJk3IDbZ7vbX91NjaIZ_O6qnPqbCmJpUgdoWuvRmRK3HWEkkZrj/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67632.html vittal korann Re: [Freesurfer] mean gyrification... https://secure-web.cisco.com/1Js1jq3EGWm32H-whdU3swtG54IceOwz0Fh3_58nbkrwZd84ZLg2urDH5DjGdwAPjaigsR9evs0_jVrtOFxn6UKZoEPeMilQUXqFa85Nobzs6W3JDRQ_ZYbrxVu5IQnXOGc5ofEAmAco9z4L7N6uTmDeHWf1Q7Sq6pNhmyxGmRIrl6W1v1ld3y3fUxP4pGMGg3iCvmVWc9mXhmdVwpT31bTQrh3bHKvep_jKB5UxRuUITJnAbQhfaiC5FBsT7xtCZGIbhG2TbniEco3vbl_NDiigAXkFxBx_jwcQDY76EKmu7i6R0_1InvPlJZDauIekV/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67633.html Douglas N. Greve Re: [Freesurfer] mean gyrific... https://secure-web.cisco.com/1518Ds0bT2RvVl-zEb5vIXvX1U_xRf4QNo-lrDGrsjFLTbyrmbuoJtAZcPgsClxUP1SYSgRTGJ9LDCEpm-ZO2Ucy5yxso1vSFyAdswTMzqiyf90I1ZKNXZR0cNTHztJW09TI2ZMBOANaDALhC1RA63YaKwMHnUJJ3ct-BMzzAinQIrZps4YuYdTqVet8yavxrT7JBdyLU5siqGLBlMCbkvWhcWFFTnntgapuQjmp--dOzAF4Ro2shppQaWaWou1Sc_nthGNMoquXqL63tjBwqT9BFvCHFgjQym5DswT2HaB2-8as_Nl8nSVBwic3Lpy0Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67634.html vittal korann Re: [Freesurfer] mean gyr... https://secure-web.cisco.com/1oOL9uCWMdAKyQi_QbRJAnUXwQD6zmJTQUsdxcXeQZ9ooXLzsbJc7KFjJUmrD6XBVTCm8ohIXRrIx45RBGW5_5hmmkOxgGy_0YbWzpPKosmvQVgLbUc2seZrYVFG5P8PU2apCONASKC1UV57TzkWgYrf9ycQXfKisbN0SeUQkbyhbnhhcLfRCL2BsGN3XBX38NWg-vINIkCCrwqlq-eb8iwxoBHwmeKChP9tRmyZlj39OFbIUMfSmfUjFT6LcuAGHGcmdhZGps0FSCJb6lNZEFnc9F5jbxx8yk7SIaGdv-xScfPxAW2kleCosy9F0mVAJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67636.html Douglas N. Greve Re: [Freesurfer] mean... https://secure-web.cisco.com/1uv3ZnOl6QPrfIG-qlulfdX6wxOPYalWdNW5bkfPinCGbhNfLxYUWkTavQ_nRHeh72Yp5NPgTOiSiObzEijvj8OtaLjnXnwhpBuTKJk46bIae6MKoBpmHkW_B6xnAPdGFKckHGYJULiCYkdkFgb79dhWkpLBWHGK687YtxCHN9xh8yBtFRM_GtFoz6_ibpMGZb3sWr-v6Vo5fjZA9oTlGMY5RszJwECVJAbAt9JDglrSBFDAEdGNEMYaiuO7JKBW4lqQSa3OPV7YhCgiuLLtliRPMVIWoe0HQGVlBGTrsrhpP_OkQzAl_JGfcmJny5uj5/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67648.html vittal korann Reply via email to
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