External Email - Use Caution
Dear 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 Douglas 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. https://secure-web.cisco.com/1XEfOrvgDwm2ivmcxJZotbNUpaeDPYzXRGyLreghU2caPdG... 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 --sum lh.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 0.6366 1.9369 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...@gmail.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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