FreeSurfer Segmentation Fault

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Bartlett, Rob

21 Mar 2023 21 Mar '23

6:50 a.m.

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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 http://secure-web.cisco.com/1ldWtsR_k8GujZ8y7If5rBkMRJurdJwyRqSfEIf5VZerYzRq... Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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Wang, Ruopeng

21 Mar 21 Mar

9:35 a.m.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

External Email - Use Caution

Kind regards, Rob Bartlett Research IT Officer University of Exeter www.exeter.ac.ukhttp://www.exeter.ac.uk/ Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bartlett, Rob

12:17 p.m.

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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 http://secure-web.cisco.com/19LYNNE_BZY4uNXsZT2DPlO-e9qSS7_qSXcEpIdeuO8BHSYd... Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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 is safe.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

External Email - Use Caution

Kind regards, Rob Bartlett Research IT Officer University of Exeter http://secure-web.cisco.com/19LYNNE_BZY4uNXsZT2DPlO-e9qSS7_qSXcEpIdeuO8BHSYd...https://secure-web.cisco.com/1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8RDQOQ3pZ9lmINvxak12OLrf02vKIYRq3XSjcv_e9WvgXdrdhu-cT1BKY3UviPQHYOIWcYPwhKd9dAkA8fBLJNtMNjlGaVT-dtkd4JrTa0LrHxhupbnMFOENigN3ohIkPMsI46DG0DmqzyRmaf7o0p1ZX22pCtgNVniFzH6x4s4g0899kNYWMp0b3YOigM6uix9s6RiWw7Suki2d2QxKGGD9tYrdEC-I_ic6CDxw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257Cdefb78c58a5e401f9f5708db2a118aa3%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150027050095991%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D6T%252FQVZCaN%252BFng3rn9s4bIy9saHBpG7X6yti4TUEGQR8%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/18jAxIaO5FmPwfh94_2bDGkdGLKQvp74tKklPupTbxDMvVJ...https://secure-web.cisco.com/10jrUgLjpsj14JOEBUVlZBCyFCsYKnP36bt5CAECqlM5OUuK6T_s2klN7-s_HjtunItXUKmtXYjTa1_sE8y7T11xKXzeLJHC_e8p1piHffMTuQgv1tOHUXeDEXdfATyZ9ZOLq9uobHs6p1eoF53vEatLHe2ZdzeViZllOoSFRvCa3bA5olxYMtobeUOlbWZr8mDS9QUtiePTpIpY3kMmOww36KR2rmKkyKiQtt6FKKn1BTfbtlWkmFdJ8g4kDFjwpicWlzKOJn2xxCcOqzN_jzSpg5jDJknAxxvZn3KXvwYzUFau2uw0IEiRD_8r2zBMvsH7KGIcosxMcAn_bov3dAQ/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%257Cdefb78c58a5e401f9f5708db2a118aa3%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150027050095991%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D2du11mAINebbZn%252Bs7LtYWdeApZwLXGLfS0ZKjALS%252B8Y%253D%26reserved%3D0

Fischl, Bruce R.,PHD

2:52 p.m.

Oh, sorry, should have read to the end of my inbox before responding. What does ls -l show for that file?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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 www.exeter.ac.ukhttp://www.exeter.ac.uk Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 is safe.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

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Kind regards, Rob Bartlett Research IT Officer University of Exeter MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.exeter.ac.ukhttps://secure-web.cisco.com/1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8RDQOQ3pZ9lmINvxak12OLrf02vKIYRq3XSjcv_e9WvgXdrdhu-cT1BKY3UviPQHYOIWcYPwhKd9dAkA8fBLJNtMNjlGaVT-dtkd4JrTa0LrHxhupbnMFOENigN3ohIkPMsI46DG0DmqzyRmaf7o0p1ZX22pCtgNVniFzH6x4s4g0899kNYWMp0b3YOigM6uix9s6RiWw7Suki2d2QxKGGD9tYrdEC-I_ic6CDxw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257Cdefb78c58a5e401f9f5708db2a118aa3%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150027050095991%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D6T%252FQVZCaN%252BFng3rn9s4bIy9saHBpG7X6yti4TUEGQR8%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

Bartlett, Rob

22 Mar 22 Mar

6:50 a.m.

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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 http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaD...https://secure-web.cisco.com/195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@MGH.HARVARD.EDU Sent: 21 March 2023 18:52 To: Freesurfer support list 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 is safe.

Oh, sorry, should have read to the end of my inbox before responding. What does ls -l show for that file?

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 http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaD...https://secure-web.cisco.com/1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%252Fsj%252F2DE57k%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...]

This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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 is safe.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaD...https://secure-web.cisco.com/1ZDWryhHgOuOlmbzRIJAkA9A56LNPhiK4TzPMmLvQmZPekxvaRNgNTKBUrk1i3K1zU-izNnBmvcK034LUfdRVrr6ZoRD01YjTRuCuDTuB1B1DIbmZMIUYZz3-XsUZjICHqoNjgPa3uwdYxMSdtouHonm0AeGohGvY4KHJ7B-MG9H43UKNl2a8vi28DQlYl-aQCbhgdaD7k8CDlGtr73D46OWeMZdQVloE7XqrP4v2qOkzwiuLCLVJQKKhkPrBj8473F0CR7QemZ9Jg8LA_eJsG_4MQcUhY4YGZLIvj4jeFb3tqP5zjep0xVp_ioygplFG/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8RDQOQ3pZ9lmINvxak12OLrf02vKIYRq3XSjcv_e9WvgXdrdhu-cT1BKY3UviPQHYOIWcYPwhKd9dAkA8fBLJNtMNjlGaVT-dtkd4JrTa0LrHxhupbnMFOENigN3ohIkPMsI46DG0DmqzyRmaf7o0p1ZX22pCtgNVniFzH6x4s4g0899kNYWMp0b3YOigM6uix9s6RiWw7Suki2d2QxKGGD9tYrdEC-I_ic6CDxw%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257Cdefb78c58a5e401f9f5708db2a118aa3%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150027050095991%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253D6T%2525252FQVZCaN%2525252BFng3rn9s4bIy9saHBpG7X6yti4TUEGQR8%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D4pY%252BXIoGc6cwKERd0I9uX97hwT9nrRFqcZhvUVhIhj8%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

[http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...]

Wang, Ruopeng

9:38 a.m.

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.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.exeter.ac.ukhttps://secure-web.cisco.com/195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent: 21 March 2023 18:52 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 is safe.

Oh, sorry, should have read to the end of my inbox before responding. What does ls -l show for that file?

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.exeter.ac.ukhttps://secure-web.cisco.com/1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%252Fsj%252F2DE57k%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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 is safe.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

External Email - Use Caution

Kind regards, Rob Bartlett Research IT Officer University of Exeter MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.exeter.ac.ukhttps://secure-web.cisco.com/1ZDWryhHgOuOlmbzRIJAkA9A56LNPhiK4TzPMmLvQmZPekxvaRNgNTKBUrk1i3K1zU-izNnBmvcK034LUfdRVrr6ZoRD01YjTRuCuDTuB1B1DIbmZMIUYZz3-XsUZjICHqoNjgPa3uwdYxMSdtouHonm0AeGohGvY4KHJ7B-MG9H43UKNl2a8vi28DQlYl-aQCbhgdaD7k8CDlGtr73D46OWeMZdQVloE7XqrP4v2qOkzwiuLCLVJQKKhkPrBj8473F0CR7QemZ9Jg8LA_eJsG_4MQcUhY4YGZLIvj4jeFb3tqP5zjep0xVp_ioygplFG/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8RDQOQ3pZ9lmINvxak12OLrf02vKIYRq3XSjcv_e9WvgXdrdhu-cT1BKY3UviPQHYOIWcYPwhKd9dAkA8fBLJNtMNjlGaVT-dtkd4JrTa0LrHxhupbnMFOENigN3ohIkPMsI46DG0DmqzyRmaf7o0p1ZX22pCtgNVniFzH6x4s4g0899kNYWMp0b3YOigM6uix9s6RiWw7Suki2d2QxKGGD9tYrdEC-I_ic6CDxw%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257Cdefb78c58a5e401f9f5708db2a118aa3%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150027050095991%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253D6T%2525252FQVZCaN%2525252BFng3rn9s4bIy9saHBpG7X6yti4TUEGQR8%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D4pY%252BXIoGc6cwKERd0I9uX97hwT9nrRFqcZhvUVhIhj8%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

Bartlett, Rob

10:06 a.m.

External Email - Use Caution

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 http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-...https://secure-web.cisco.com/1Ao_nmhMWqLMJ0SApqz0FgGFfr6xrL6fjzJm5-0MmLUs0YDiRm7kfdIlpEAYsrzJfs2UyJiQGCDucny_3mQF-l6JcA_ZBHP5Q2UL1CWFplbYHtHTIqfCBHARFa75kMbdhHbkurMyAvTTcIUs5sJkiumTevGCyOG_dEBCnonPQh3VCUlRmtf4oisqWYysvjoREOBNS_ksLhehgjL1zRcW0JgBOApEsM5Vl63vj3UUnsI_INIrhIKn_ZhckXJDPlXAjIef05KmS1FGt_MUaDnXf8_FwSZLFB3jTcKB_JaOibuE0dZxvnGPB4BiA25JoqN4rq9e_2OFf7flVBzWH17Ufjw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@MGH.HARVARD.EDU Sent: 22 March 2023 13:38 To: Freesurfer support list 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 is safe.

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.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@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

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 is safe.

Oh, sorry, should have read to the end of my inbox before responding. What does ls -l show for that file?

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-...https://secure-web.cisco.com/1xMoOiUQINoC-SB4fyyf_O8IlcMxGLNTcUS5vOWA3o6eMKXnkiz-XPE6pVRuMlBz5EE9ctI3kDdVdLqTzAmBHJ2Eu62HiJsQQ5I89BvGibkCFo_KZBLMsHUTYYl0AEQZvwmvf9eZCrLlsfhxvdcUbFrRIGjaXMBbDyk4XGlw4iGOu0GKUbPq3DyyoAAHM0CoRNGlr-IFqa4ZkEARnqTuR0ZpzlvZ7PoEYxgrzmqMrlvrDXiTsutPP0j9B_SHhyIP2Pwg7FDuwh8LwdUsAbCveQNjTXlNp8xbLIolW_l78h5hlLXK_7U7rdOHkQShRUvWAZvdqamq9qmGVVQd1z_xPdg/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257C627ae2f2d00e4535c78d08db2a3dc38f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150216985257453%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%2525252Fsj%2525252F2DE57k%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DqIHdcLguIV%252BWdRRc2RLel8cAqr2czCL5qPFho8uKpxM%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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 is safe.

Can you post the full freeview command that you ran?

Ruopeng

On Mar 21, 2023, at 6:50 AM, Bartlett, Rob <R.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

External Email - Use Caution

Kind regards, Rob Bartlett Research IT Officer University of Exeter MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-...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-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/15BqffUKP63tGgtjI3LLwLHwEyi1J1cGcP6IvUULcZarpPd...https://secure-web.cisco.com/1IpJ4881U5REQT0zQSXNOVQT_vdbk-_BUflFNSfBfth7YWZUQfUyBW5AoUDBfq54b4J3LPGPZeqct5LUk9n94VYinLIAsXoMZmkTw8eW5B77iDAvjYptKbx3Q4Xu6PP7V3mzUysWFynmedoQuOz6U_Qs3oDkHNvi9GUi983VltOThd9hRBReSkPwCC5VncaaeLY8gj2BLT4tQ2OQujOlbfLQnr-veoajpZdDP5Jy03DFWNe4lzpbDqzxKIjphutj01J5A48dcwvc_X_4Rid5p6Q/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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15BqffUKP63tGgtjI3LLwLHwEyi1J1cGcP6IvUULcZarpPd...https://secure-web.cisco.com/1kqxIRwBNr2PwWOA5BirUbE5aiMIizmhmwTlEBGTG4IyyOXqikEmi6R8suQP_unOxBKFfrjXfE2USO8lY_E6hxw6dGK8BdskLRECck-Z8j9Ygv8_AOOCAsVFMaziUnBYhZJiiJ-ICl-MC3qEAX4lc--gHWM7EqkVHjBh6hdhxsx-N3398dYhVnu_wXHKiUN1JUcErDPIRzRF5aBZKWv9hUGAXw_y49w1eHIbh2iK-MOkAjrIvc3Ml37jyvHmaGAZNFbr11Et1RMkh3hPAI0H6jqPQrJYYMy3O8bd83wlJGS4gFaiVV0Pp3ExrahDtIjmzT6I7p96JAdxmD8ibyQzcqw/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

Zhao, Don

1:30 p.m.

New subject: Password ubuntu password

External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

[[***CAUTION*** This email originated from outside of Messiah University]]

External Email - Use Caution 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcr...https://secure-web.cisco.com/1Ao_nmhMWqLMJ0SApqz0FgGFfr6xrL6fjzJm5-0MmLUs0YDiRm7kfdIlpEAYsrzJfs2UyJiQGCDucny_3mQF-l6JcA_ZBHP5Q2UL1CWFplbYHtHTIqfCBHARFa75kMbdhHbkurMyAvTTcIUs5sJkiumTevGCyOG_dEBCnonPQh3VCUlRmtf4oisqWYysvjoREOBNS_ksLhehgjL1zRcW0JgBOApEsM5Vl63vj3UUnsI_INIrhIKn_ZhckXJDPlXAjIef05KmS1FGt_MUaDnXf8_FwSZLFB3jTcKB_JaOibuE0dZxvnGPB4BiA25JoqN4rq9e_2OFf7flVBzWH17Ufjw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Sent: 22 March 2023 13:38 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcr...https://secure-web.cisco.com/1Wml9lhUT26ZPphpwU0GnmdMmVs2KQzl8N9RhG1zIdq6JetDNCV9xUtgU-ktF1Ye8DdXwEG04fN7UryW-9ljeGo-j5EvfdIHD4Y4psB6I_l2_UHO9G5As1kdNURXLPsCndXFvuBmdUzTmlWdb4JAOmChaVWd0U76KxDE4O4Qrob5bGipgAjPawbpqCJ_SL1lwulZSiC7ZRnTdAKo95GTkqj731rJ8cYwsnVC85AxCThO8PqlBhgR0MG8k8TeIq0Ku-wpWyp7UapbyvaNwFUI1crqpU9UQk9Pp1zrOmmovCFnrVBOqC4nE7YjNlT6yR98y_9h0_yrOOFthcUK2XJK80A/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257CR.Bartlett2%25252540exeter.ac.uk%2525257Cab38191defec41cba9f908db29ee295f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638149875083781919%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DB0%2525252B7hoeo%2525252Bfa%2525252BUgSXzduACwplHUD9z52ah%2525252B1AegiL4vo%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DKRUppguaaFWZ9DGc4VAB9V0A731irntFz68jmREY4Hw%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE

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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/171EG5Xbe71Hukd6GqPyZPvblqCEeoxzcg1EjZPHtSfNSxcr...https://secure-web.cisco.com/1xMoOiUQINoC-SB4fyyf_O8IlcMxGLNTcUS5vOWA3o6eMKXnkiz-XPE6pVRuMlBz5EE9ctI3kDdVdLqTzAmBHJ2Eu62HiJsQQ5I89BvGibkCFo_KZBLMsHUTYYl0AEQZvwmvf9eZCrLlsfhxvdcUbFrRIGjaXMBbDyk4XGlw4iGOu0GKUbPq3DyyoAAHM0CoRNGlr-IFqa4ZkEARnqTuR0ZpzlvZ7PoEYxgrzmqMrlvrDXiTsutPP0j9B_SHhyIP2Pwg7FDuwh8LwdUsAbCveQNjTXlNp8xbLIolW_l78h5hlLXK_7U7rdOHkQShRUvWAZvdqamq9qmGVVQd1z_xPdg/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257Cr.bartlett2%25252540exeter.ac.uk%2525257C627ae2f2d00e4535c78d08db2a3dc38f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638150216985257453%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%2525252Fsj%2525252F2DE57k%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DqIHdcLguIV%252BWdRRc2RLel8cAqr2czCL5qPFho8uKpxM%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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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.Bartlett2@exeter.ac.ukmailto:R.Bartlett2@exeter.ac.uk> wrote:

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Zhao, Don

2 p.m.

New subject: the virtual machine RE: Password ubuntu password

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"login as the user "developer" in the login menu. Get the password by sending an email request to the freesurfer help list." Hi, freesurfer help list. May I have the password, please? Thanks, Don

Zhao, Don

23 Mar 23 Mar

2:04 p.m.

New subject: the virtual machine developer password RE: Password ubuntu password

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The Freesurfer VirtualBox instructions state: "login as the user "developer" in the login menu. Get the password by sending an email request to the freesurfer help list." Despite asking this question multiple times, I am still unsure of how to obtain the password. Can anyone provide assistance with this? Thank you in advance. Sincerely, Don

From: Zhao, Don Sent: Wednesday, March 22, 2023 2:00 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: the virtual machine RE: Password ubuntu password

"login as the user "developer" in the login menu. Get the password by sending an email request to the freesurfer help list." Hi, freesurfer help list. May I have the password, please? Thanks, Don

Fischl, Bruce R.,PHD

21 Mar 21 Mar

9:58 a.m.

Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a reasonable size?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bartlett, Rob Sent: Tuesday, March 21, 2023 6:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FreeSurfer Segmentation Fault

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.

Kind regards, Rob Bartlett Research IT Officer University of Exeter www.exeter.ac.ukhttp://www.exeter.ac.uk Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

Bartlett, Rob

12:14 p.m.

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Hi Bruce, here is the output:

Volume information for tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 12.00 msec, TE: 4.76 msec, TI: 4.76 msec, flip angle: 20.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -4.5707 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 40.4204 : x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 6.8018

talairach xfm : tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 -0.0000 0.0000 123.4293 0.0000 0.0000 1.0000 -87.5796 -0.0000 -1.0000 0.0000 134.8018 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 0.0000 123.4293 0.0000 0.0000 -1.0000 134.8018 -0.0000 1.0000 -0.0000 87.5796 -0.0000 -0.0000 -0.0000 1.0000

Kind regards, Rob Bartlett Research IT Officer University of Exeter http://secure-web.cisco.com/1T3UxPKF0R9TnBw_2ltCSMTfEH3AvjHM2FInqeG43YNbD7OD... Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1qEf3w94plVSPmCQ1FMfRUITvU3KTNbP7UPtrGs_S99-pRbZ...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce R.,PHD Sent: Tuesday, March 21, 2023 1:58 PM To: Freesurfer support list 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 is safe.

Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a reasonable size?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bartlett, Rob Sent: Tuesday, March 21, 2023 6:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FreeSurfer Segmentation Fault

Kind regards, Rob Bartlett Research IT Officer University of Exeter http://secure-web.cisco.com/1T3UxPKF0R9TnBw_2ltCSMTfEH3AvjHM2FInqeG43YNbD7OD...https://secure-web.cisco.com/1jV0EeaMmsCE9O-8_cZWhqLbCR0xN8vormwkmUZXvKhBAU7ITQ_xwkeAtRSxHXgtE4FLF1ZdMudpuJ_GaZ5qf2Q6fnnWBhdr6Ewp_tV2M0IE9aOZcWfz4ae_hcRKPMPWLaLD8sCxVVAxpRHzrNVxgjDXCESzfYMn1xmSEnmYhTqty5cApn6RNmgkoxM5t6il4CpX5Sn3pd1UPFg6VrYFPnS23436ugaRLycrwgeUFNShTOhaLf6vYUKT4qMvjbHmd6f1cge3NNr8gf_t3-E6A6qJg5TGu7Q1QNYZn-nRTC1aqqQvW1L3-CEtLQkrGygDLrd2L7oUIpgp07NDXSdFPnQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C57495c7f9c064f8a114208db2a1484c6%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150039840170667%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D5ftuSH9roU8gefU5PdIaSrDO4ssgwDd2%252BBA0f6dWya8%253D%26reserved%3D0 Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

Fischl, Bruce R.,PHD

2:51 p.m.

Hmm, that all looks fine. And what is your freeview command line that crashes?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bartlett, Rob Sent: Tuesday, March 21, 2023 12:14 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

External Email - Use Caution Hi Bruce, here is the output:

talairach xfm : tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 -0.0000 0.0000 123.4293 0.0000 0.0000 1.0000 -87.5796 -0.0000 -1.0000 0.0000 134.8018 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 0.0000 123.4293 0.0000 0.0000 -1.0000 134.8018 -0.0000 1.0000 -0.0000 87.5796 -0.0000 -0.0000 -0.0000 1.0000

Kind regards, Rob Bartlett Research IT Officer University of Exeter www.exeter.ac.ukhttp://www.exeter.ac.uk Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1qEf3w94plVSPmCQ1FMfRUITvU3KTNbP7UPtrGs_S99-pRbZ...] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce R.,PHD Sent: Tuesday, March 21, 2023 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault

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Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a reasonable size?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bartlett, Rob Sent: Tuesday, March 21, 2023 6:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FreeSurfer Segmentation Fault

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Bartlett, Rob
Fischl, Bruce R.,PHD
Wang, Ruopeng
Zhao, Don