Dear Eugenio It has been working very well. It stopped working suddenly. It produce two error containing text file within 10 seconds. I tried to install fresh matlab runtime2012b. However, I have not seen any change. The error is bumped as attached.

There are no output file except two errors that are saved in the Users/myuserid_directory/

I would appreciate if you please help me in this regard.

On Mon, May 22, 2017 at 5:39 PM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

Thanks, Mamun. Do you bump into this error with every subject you process? Also, what’s the output before the error? Cheers, /Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 20 May 2017, at 02:08, Md. Mamun Al-Amin mdalaminbadal@gmail.com wrote:

Hello FreeSurfer Developers,

I'm attempting to compute hippocampal subfield segmentation. Unfortunatelty I found following errors.

---

   Segmentation violation detected at Sat May 20 10:45:37 2017

---

Configuration: Crash Decoding : Disabled Current Visual : None Default Encoding: ISO-8859-1 MATLAB Root : /Applications/freesurfer/MCRv80 MATLAB Version : 8.0.0.783 (R2012b) Operating System: Darwin 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 58 Stepping 9, GenuineIntel Window System : No active display

Fault Count: 1

Abnormal termination: Segmentation violation

Register State (from fault): RAX = 0000000000000000 RBX = 0000000103310000 RCX = 0000000000000006 RDX = 0000000103313a00 RSP = 000000010fc39e80 RBP = 000000d0ffffffff RSI = ffffffffffffffff RDI = 0000000000000005

R8 = 0000000000000000 R9 = 0000000110323852 R10 = 0000700002d27480 R11 = 0000700002d274e0 R12 = 0000000000000005 R13 = 000000001c004121 R14 = 0000000000000246 R15 = 0000000110500160

RIP = 0000700002d27b98 RFL = 0000700002d27b60

CS = 000000010f91fd54 FS = 0000700002d27360 GS = 0000000000000005

Stack Trace (from fault): [ 0] 0x0000000101e61e46 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150 [ 1] 0x0000000101e62af1 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665 fl_diag_terminate+000321 [ 2] 0x0000000101e64c34 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180 _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100 [ 3] 0x0000000105ed825e /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998 mnTrapCtrlc+000254 [ 4] 0x0000000105ed9d24 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852 _Z32mnRunPathDependentInitializationv+003492 [ 5] 0x0000000105eda13d /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901 _Z32mnRunPathDependentInitializationv+004541 [ 6] 0x0000000105eda7f5 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621 _Z32mnRunPathDependentInitializationv+006261 [ 7] 0x0000000105eda945 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957 mnFatalSignalHandler+000149 [ 8] 0x00007fffa5b60b3a /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+000026 [ 9] 0x00000004ffffffff /usr/lib/system/libsystem_platform.dylib+18446603359210840063

If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /Users/mdmamunalamin/matlab_crash_dump.5756-1 **

MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 5756 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $a

I would like to draw your kind attention regarding this.

--

Kind regards

Md. Mamun Al-Amin

PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Eugenio Here is the log file. Thanks in advance.

Kind regards Mamun

On Mon, May 22, 2017 at 7:05 PM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

Thanks! Can you please send the log files: recon-all.log and hippocampal-subfields-T1.log, which can be found in $SUBJECTS_DIR/[SUBJECT_NAME]/scripts/ ? Cheers, /Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 22 May 2017, at 09:49, Md. Mamun Al-Amin mdalaminbadal@gmail.com wrote:

Dear Eugenio It has been working very well. It stopped working suddenly. It produce two error containing text file within 10 seconds. I tried to install fresh matlab runtime2012b. However, I have not seen any change. The error is bumped as attached.

There are no output file except two errors that are saved in the Users/myuserid_directory/

I would appreciate if you please help me in this regard.

On Mon, May 22, 2017 at 5:39 PM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

...

Thanks, Mamun. Do you bump into this error with every subject you process? Also, what’s the output before the error? Cheers, /Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 20 May 2017, at 02:08, Md. Mamun Al-Amin mdalaminbadal@gmail.com wrote:

Hello FreeSurfer Developers,

I'm attempting to compute hippocampal subfield segmentation. Unfortunatelty I found following errors.

---

   Segmentation violation detected at Sat May 20 10:45:37 2017

---

Configuration: Crash Decoding : Disabled Current Visual : None Default Encoding: ISO-8859-1 MATLAB Root : /Applications/freesurfer/MCRv80 MATLAB Version : 8.0.0.783 (R2012b) Operating System: Darwin 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 58 Stepping 9, GenuineIntel Window System : No active display

Fault Count: 1

Abnormal termination: Segmentation violation

Register State (from fault): RAX = 0000000000000000 RBX = 0000000103310000 RCX = 0000000000000006 RDX = 0000000103313a00 RSP = 000000010fc39e80 RBP = 000000d0ffffffff RSI = ffffffffffffffff RDI = 0000000000000005

R8 = 0000000000000000 R9 = 0000000110323852 R10 = 0000700002d27480 R11 = 0000700002d274e0 R12 = 0000000000000005 R13 = 000000001c004121 R14 = 0000000000000246 R15 = 0000000110500160

RIP = 0000700002d27b98 RFL = 0000700002d27b60

CS = 000000010f91fd54 FS = 0000700002d27360 GS = 0000000000000005

Stack Trace (from fault): [ 0] 0x0000000101e61e46 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150 [ 1] 0x0000000101e62af1 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665 fl_diag_terminate+000321 [ 2] 0x0000000101e64c34 /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180 _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100 [ 3] 0x0000000105ed825e /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998 mnTrapCtrlc+000254 [ 4] 0x0000000105ed9d24 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852 _Z32mnRunPathDependentInitializationv+003492 [ 5] 0x0000000105eda13d /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901 _Z32mnRunPathDependentInitializationv+004541 [ 6] 0x0000000105eda7f5 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621 _Z32mnRunPathDependentInitializationv+006261 [ 7] 0x0000000105eda945 /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957 mnFatalSignalHandler+000149 [ 8] 0x00007fffa5b60b3a /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+000026 [ 9] 0x00000004ffffffff /usr/lib/system/libsystem_platform.dylib+18446603359210840063

If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /Users/mdmamunalamin/matlab_crash_dump.5756-1 **

MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 5756 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $a

I would like to draw your kind attention regarding this.

--

Kind regards

Md. Mamun Al-Amin

PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

--

Kind regards

Md. Mamun Al-Amin

PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072 <matlab_crash_dump.33234-1><matlab_crash_dump.33269-1>____ ___________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.