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 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.
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html
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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...@*MailScanner has detected a possible fraud attempt
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<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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* Re: [Freesurfer] Mean Gyrification index
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vittal korann
*
o Re: [Freesurfer] Mean Gyrification index Douglas N. Greve
o [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
o
+ 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
*
o Re: [Freesurfer] mean gyrific...
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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...
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Douglas N. Greve
*
o Re: [Freesurfer] mean gyrific...
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vittal korann
o
+ 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
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