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:
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
www.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE
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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
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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.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.
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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