External Email - Use Caution 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_2ltCSMTfEH3AvjHM2FInqeG43YNbD7OD0itZmsPW_1S8vtTQoDMMAeJby8Zqgl9nb4m_yLwjeBMDi168NweC6SZzTEObKbV7t-NL4N7sEeH163BzBaKKKlWUDZTrUrxny6ojH9KCi6e2p6kVBz0U0fyO1v1U3KAJcstD5wQafDyf17gEAqCM6Oh-2bmN3f1ZmNQrXymTVERCecg4xfaQP4AgU0QWvcsUodezJ9BOYnFLVlAIR-nt0V_xODXsa29KkWsdFyTy_GpHRnGZ7EQ77RY3b9Ks2PrrOjaBCSF2yUglS60XWj8Ooxpo2RRECHg-C1I4nOw/http%3A%2F%2Fwww.exeter.ac.uk Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/1qEf3w94plVSPmCQ1FMfRUITvU3KTNbP7UPtrGs_S99-pRbZ55SFEcS7XZZ0XIh4VC_M5EYEfDLw9U7BeTl1tz6kyckI0GFpwzy4ZVmV8NJpbIqjsgwWHBgFZhoJmeV2gPm7zWP5o5SPtP1fNHLOsNA__lNJ3eYA5QiJCQKii7aaly3AA-4AAi6CU9IXYFwKrWt2XjfE44z6Q9aQQ6igCyZ4j5bmidXCyBp2zadwM3EDD8SmIzWwM28cvNKvbVnbEwDMDNXWvPvYE0uyc0dxYwfwy1GpOEf1IGV8-KzLT2B1vf0wFmf4WjQMGitf33TW8_XP61FvUV0atf_FRxof5lg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif] 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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-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 6:50 AM To: freesurfer@nmr.mgh.harvard.edu<mailto: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. 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/1T3UxPKF0R9TnBw_2ltCSMTfEH3AvjHM2FInqeG43YNbD7OD0itZmsPW_1S8vtTQoDMMAeJby8Zqgl9nb4m_yLwjeBMDi168NweC6SZzTEObKbV7t-NL4N7sEeH163BzBaKKKlWUDZTrUrxny6ojH9KCi6e2p6kVBz0U0fyO1v1U3KAJcstD5wQafDyf17gEAqCM6Oh-2bmN3f1ZmNQrXymTVERCecg4xfaQP4AgU0QWvcsUodezJ9BOYnFLVlAIR-nt0V_xODXsa29KkWsdFyTy_GpHRnGZ7EQ77RY3b9Ks2PrrOjaBCSF2yUglS60XWj8Ooxpo2RRECHg-C1I4nOw/http%3A%2F%2Fwww.exeter.ac.uk<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-xjjxoXAf6UcUYwpLuh88juFgvzCjlQx1E2e5B_ccRw64OO8yofsPIRbtZ9ZtKGOy2pgw20hVbt9xCTUoIk6utGG1K6G_K_-rK0-NG2vdkGkYYSscwlwtxK58zuaMQqmnsUVY_32xHpaU2rsvfIVQHYxnqqPODe0gUXaadMq3BevHC1xXp2hNDNDNnZZZ5mLG7HjLVFPagt_3mjNY2e3_ul7sZN3crwabzwKP7hKWiOynm55ZU0THvS4Uh1u5kl04SCAzsC4JEubOuz7h2C3qB-xqCHIAEnDgpTIAGHvtIWYV5dWg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif] 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. 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