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I have followed the virtual machine setup for virtual box freesurfer
installation; but it ask me the password for the developer account.
Which is the password?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bartlett, Rob
Sent: Wednesday, March 22, 2023 10:06 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
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I get the same error when trying to open any files with the .mgz extension that
I have tried so far.
Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
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Laver Building, North Park Road, Exeter, EX4 4QE
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Wang, Ruopeng
<rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>>
Sent: 22 March 2023 13:38
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
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Have you tried loading a different volume in the same folder? Such as
brain.mgz. Will you get the same error?
On Mar 22, 2023, at 6:50 AM, Bartlett, Rob
<r.bartle...@exeter.ac.uk<mailto:r.bartle...@exeter.ac.uk>> wrote:
External Email - Use Caution
Hi Bruce,
No problem, thanks for getting back to me quickly.
Here is the output of -l against the file:
brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30 2018 brainmask.mgz
Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
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Laver Building, North Park Road, Exeter, EX4 4QE
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: 21 March 2023 18:52
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
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Oh, sorry, should have read to the end of my inbox before responding. What
does ls -l show for that file?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
External Email - Use Caution
Hi Ruopeng,
This is the command I have been using: freeview
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz
I get the same result when I open freeview and select the volume through the
GUI.
Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
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Laver Building, North Park Road, Exeter, EX4 4QE
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From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or open attachments unless you recognise the sender and know the content
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Can you post the full freeview command that you ran?
Ruopeng
On Mar 21, 2023, at 6:50 AM, Bartlett, Rob
<r.bartle...@exeter.ac.uk<mailto:r.bartle...@exeter.ac.uk>> wrote:
External Email - Use Caution
Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where
Freeview crashes with a segmentation fault when loading a .mgz volume file. The
files I have been trying to open are part of the tutorial dataset.
Build Stamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]:
segfault at ad0 ip 00005613a159eb5d sp 00007fb580f68d00 error 4 in
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63
c9 48 8d 14 96 48 8d 0c 8e <f3> 0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]:
segfault at fe1a641 ip 00005613a159eb5d sp 00007fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63
c9 48 8d 14 96 48 8d 0c 8e <f3> 0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps:
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps:
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps:
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps:
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps:
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps:
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps:
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps:
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00
error:0
Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
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http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcrF_ary5F2DoFbVUYU1_MSzwS5v9rvsmWzXqslw7lirGPduR5HFRTdGWd4jiS1FbKYuFuLx3XZxzuqmddYK9gYH0-jf5mnT3uFnude2WmZuUkaGlUDiN3Nv1jAtb_G_Dlp9MRg_l72REi3idAej-HfHGJWzboPXPEvURKZKrOBTSlLXm6k9VZcrXiC82NQJ_I1FOz-WYIDARiaKvwUMvpXLATOr0uZurhCI9jpEguWYCOA85QnJJzgvU8mUMlbFv5Nws_iGEqiNor6JdmWGIEzmaEeu-z2FKmIQQxh4jg/http%3A%2F%2Fwww.exeter.ac.uk<https://secure-web.cisco.com/1G2i1V9hLS9hE3HuqPY12HerCWcgW6e4AYrQqWQld-g40EuUpAWvxYsubs7DiVAd23RV0GNArf3l5eSFjx24UgANGWLAJsvgsVDOOz4byZHkhQGN-h37phNNc3LQyOwn8hcFHpUNMMLDwbLJ8XOskMdlqmz6fuE8vkKUQhP0j_jUio1rSZmpbfkUroQYLUycjIa8Qge-wQaDNqnqBzYPplUyuldcZ3ULqt99PUGlYSjG8WguP46Lm6fpmRDtxihS3k4bAZvSrwrpn09GVXJPqAA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1ZDWryhHgOuOlmbzRIJAkA9A56LNPhiK4TzPMmLvQmZPekxvaRNgNTKBUrk1i3K1zU-izNnBmvcK034LUfdRVrr6ZoRD01YjTRuCuDTuB1B1DIbmZMIUYZz3-XsUZjICHqoNjgPa3uwdYxMSdtouHonm0AeGohGvY4KHJ7B-MG9H43UKNl2a8vi28DQlYl-aQCbhgdaD7k8CDlGtr73D46OWeMZdQVloE7XqrP4v2qOkzwiuLCLVJQKKhkPrBj8473F0CR7QemZ9Jg8LA_eJsG_4MQcUhY4YGZLIvj4jeFb3tqP5zjep0xVp_ioygplFG%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8RDQOQ3pZ9lmINvxak12OLrf02vKIYRq3XSjcv_e9WvgXdrdhu-cT1BKY3UviPQHYOIWcYPwhKd9dAkA8fBLJNtMNjlGaVT-dtkd4JrTa0LrHxhupbnMFOENigN3ohIkPMsI46DG0DmqzyRmaf7o0p1ZX22pCtgNVniFzH6x4s4g0899kNYWMp0b3YOigM6uix9s6RiWw7Suki2d2QxKGGD9tYrdEC-I_ic6CDxw%2525252Fhttps%252525253A%252525252F%252525252Feur03.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttp%25252525253A%25252525252F%25252525252Fwww.exeter.ac.uk%25252525252F%2525252526data%252525253D05%25252525257C01%25252525257Cr.bartlett2%252525252540exeter.ac.uk%25252525257Cdefb78c58a5e401f9f5708db2a118aa3%25252525257C912a5d77fb984eeeaf321334d8f04a53%25252525257C0%25252525257C0%25252525257C638150027050095991%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C3000%25252525257C%25252525257C%25252525257C%2525252526sdata%252525253D6T%25252525252FQVZCaN%25252525252BFng3rn9s4bIy9saHBpG7X6yti4TUEGQR8%25252525253D%2525252526reserved%252525253D0%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257C627ae2f2d00e4535c78d08db2a3dc38f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150216985257453%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253D4pY%2525252BXIoGc6cwKERd0I9uX97hwT9nrRFqcZhvUVhIhj8%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D0SAY987XO5bvlelkXBnLSY7HOLRLCAf7yv1CFAm3i90%253D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6UcUYwpLuh88juFgvzCjlQx1E2e5B_ccRw64OO8yofsPIRbtZ9ZtKGOy2pgw20hVbt9xCTUoIk6utGG1K6G_K_-rK0-NG2vdkGkYYSscwlwtxK58zuaMQqmnsUVY_32xHpaU2rsvfIVQHYxnqqPODe0gUXaadMq3BevHC1xXp2hNDNDNnZZZ5mLG7HjLVFPagt_3mjNY2e3_ul7sZN3crwabzwKP7hKWiOynm55ZU0THvS4Uh1u5kl04SCAzsC4JEubOuz7h2C3qB-xqCHIAEnDgpTIAGHvtIWYV5dWg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1WnP5N7l11jXi_sAa0Ks1y2fTQJG1K3bpJ460zLrfrIZ3Y3ILxSv_dI5wuhF5B0JDXu5LNM2ftFohx9hfzPaF85R9H-od2nhLm8DVExzLOEA9yhp9FeK6jdUBDth-Wd5UGNlVRI3c3ktEOMN9ngBDNRxkmxd1bEQ_xfn33D01yFjakvJbPe9QvYbDqjjZwj0Secyfd-K357YbjwYfXMy3U--MAQfngyE-T4XJjnAj5xOLr6uybAJQ8r2hguk2mLR8J470YvinmO9gDvnsNZvzovxRnp6lVJJnP-HpPHKl0UZWPDv0oulcYAj9s9ciP1wESscphutNkWH42SOSiK875w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/11EogH9BQ3jUfDSC8ZphtJyeHflnE8ZDva3lGaXGUc_K-oMEC3F_z7VoFIEcT1MGER8mU2pXWZ-ARGeMMOvsY4o3AtfL5n42RooCEh_ccKFPKxM07aurLMdelKWF1piIbGWX0tv01SguXMm8u0u0iB8QnAATuK9sz1pf2VsrKUfbJq6vr5DezXfua_BBiP0O8DlBEuGjbRSWAhg1IrpaysRnmmDa8QDDA8hVkPAl2tbjSzSVskYJQDUNA2RUP9MJDAO_qg3MJ4P2--lIFPhXWow/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1d5H3T9IJdyyz1u4bRXirreQSzR6y69S-uxf6uJreLBQfSO05o90NnyM2euzzsr4QOR-InRdkdc0_1U4PTrYC7UBtY2KC5Ndyz_cSgwSJJgA_fsiTpWHrXCQbuGq1sl7PgnHX6TqQnvWH8A0k7MFooEarE1sPvCyB5kyQuBJCNhYBHq-u6fshaRIP1a3BTHHpQf2LVVXJGn447mTnb1KrFyFmiL9OqswiuvyjW-cN4XczqofQG_0C6sQXF6Ix9OgVtvV5WPl7MBSTFDfAQpP9vV2uFfOAnhaQmClmdVTDbMg2TnECia9xnDIIxC3NW5rU%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F10jrUgLjpsj14JOEBUVlZBCyFCsYKnP36bt5CAECqlM5OUuK6T_s2klN7-s_HjtunItXUKmtXYjTa1_sE8y7T11xKXzeLJHC_e8p1piHffMTuQgv1tOHUXeDEXdfATyZ9ZOLq9uobHs6p1eoF53vEatLHe2ZdzeViZllOoSFRvCa3bA5olxYMtobeUOlbWZr8mDS9QUtiePTpIpY3kMmOww36KR2rmKkyKiQtt6FKKn1BTfbtlWkmFdJ8g4kDFjwpicWlzKOJn2xxCcOqzN_jzSpg5jDJknAxxvZn3KXvwYzUFau2uw0IEiRD_8r2zBMvsH7KGIcosxMcAn_bov3dAQ%2525252Fhttps%252525253A%252525252F%252525252Feur03.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fmail.nmr.mgh.harvard.edu%25252525252Fmailman%25252525252Flistinfo%25252525252Ffreesurfer%2525252526data%252525253D05%25252525257C01%25252525257Cr.bartlett2%252525252540exeter.ac.uk%25252525257Cdefb78c58a5e401f9f5708db2a118aa3%25252525257C912a5d77fb984eeeaf321334d8f04a53%25252525257C0%25252525257C0%25252525257C638150027050095991%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C3000%25252525257C%25252525257C%25252525257C%2525252526sdata%252525253D2du11mAINebbZn%25252525252Bs7LtYWdeApZwLXGLfS0ZKjALS%25252525252B8Y%25252525253D%2525252526reserved%252525253D0%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257C627ae2f2d00e4535c78d08db2a3dc38f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150216985257453%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DiPqFFzgeA05mEMCgkBsMGdJpR0yjFIU0wU0lFC886bA%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252Bsm67kntt4AnDE0HnzUhQxeniIUkHSRJ81svcATjpCY%253D%26reserved%3D0>
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1WnP5N7l11jXi_sAa0Ks1y2fTQJG1K3bpJ460zLrfrIZ3Y3ILxSv_dI5wuhF5B0JDXu5LNM2ftFohx9hfzPaF85R9H-od2nhLm8DVExzLOEA9yhp9FeK6jdUBDth-Wd5UGNlVRI3c3ktEOMN9ngBDNRxkmxd1bEQ_xfn33D01yFjakvJbPe9QvYbDqjjZwj0Secyfd-K357YbjwYfXMy3U--MAQfngyE-T4XJjnAj5xOLr6uybAJQ8r2hguk2mLR8J470YvinmO9gDvnsNZvzovxRnp6lVJJnP-HpPHKl0UZWPDv0oulcYAj9s9ciP1wESscphutNkWH42SOSiK875w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1To4CZv1jSmQ2BoXTKUlGYLaHM8Hdj2PROQoti7NY_yU-7weDeTl9OXTK3ealZUPKplp1Mw2bf6llUg0tJDkRi5YE0v06HHMnNgfI7BtY76pSbEcvatYiTFul31-eNHIcHPl_N13aczMs_KzQuNwkKnnoWhC2FekmcRzSR_p0PWHlsmq_WkAD2iSmYn2FZZjIH8z2Y8Z8St1dGd-QiTdNr3Pyo8S_kPhZ6s6Si5rdzDwMnEBg-bd4V_Vk4jcHhsh0p_KuBSMX8hx1vld3KqN2OobJ-f5vGyUL7oQf2unIyRqtfeRwdWU0FJgkYxuyQNqaLXptIMgQOqw7eZZepSOxUQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DA5EpPzhrUeWybOZEx%252FdHqa6Vl8ZI7%252FHfmdzHGjKsYf0%253D%26reserved%3D0>
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