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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
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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
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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-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>
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