[Freesurfer] Segment subregion error
External Email - Use Caution Hi Freesurfer experts, I have been encountering following errors after running segment_subregions command. I am using freesurfer version 7.3.2, Recon -all -all has been done with the option -cm segment_subregions thalamus --cross sub-0049 Step 1: preprocessing inputs for thalamus segmentation Running command: mri_convert /var/folders/dl/1zpqwlt95bnfb3ydwm2mqd1wgn/T/tmp8ppe_a7y/tempImage.mgz /var/folders/dl/1zpqwlt95bnfb3ydwm2mqd1wgn/T/tmp8ppe_a7y/tempImage.mgz -odt float -rt cubic -vs 0.5 0.5 0.5 Preprocessing took 22 seconds Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/Applications/freesurfer/7.3.2/python/scripts/segment_subregions", line 99, in subregions.run_cross_sectional(args.structure, parameters) File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' (base) abdullah@BadaliMac recon-all % Kind regards *Md. Mamun Al-Amin, PhD* *---* *Postdoctoral Fellow* *Stark Neuroscience Research Institute* *Indiana University School of Medicine* *320 W. 15th Street, NB Bldg Rm 103* *Indianapolis, IN 46202* ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] segment_subregions failed
External Email - Use Caution Hi Freesurfer experts, I have been trying to segment thalamus using segment_subregions command available in freesurfer 7.3.2. Unfortunately, I have been encountering the following error. IN-NSCC-050385:~ mdalamin$ segment_subregions thalamus --cross sub-0023 Step 1: preprocessing inputs for thalamus segmentation Running command: mri_convert /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz -odt float -rt cubic -vs 0.5 0.5 0.5 Preprocessing took 6 seconds Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/Applications/freesurfer/7.3.2//python/scripts/segment_subregions", line 99, in subregions.run_cross_sectional(args.structure, parameters) File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Any suggestions to troubleshoot this problem? Kind regards *Md. Mamun Al-Amin, PhD* *---* *Postdoctoral Fellow* *Stark Neuroscience Research Institute* *Indiana University School of Medicine* *320 W. 15th Street, NB Bldg Rm 103* *Indianapolis, IN 46202* ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Freeview error
External Email - Use Caution Dear Experts I have been encountered a problem opening Freeview window in Mac Terminal. Could you please help me troubleshooting this problem? Here is the screenshot. Thanks in advance. -- Kind regards Md. Mamun Al-Amin -- *PhD Candidate, Queensland Brain Institute* *The University of Queensland* *Building 79, St Lucia QLD 4072* *https://qbi.uq.edu.au/profile/877/md-mamun-al-amin <https://qbi.uq.edu.au/profile/877/md-mamun-al-amin>* ___ 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.
Re: [Freesurfer] Hippocampal subfield segmentation error
Hi Eugenio
It is working.
Thank you very much.
Kind regards
Mamun
On Tue, Sep 19, 2017 at 7:55 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> Hi Mamun,
>
> There is a little bug in the script.
>
> I’ll fix the dev version ASAP, but rather than downloading a gigabyte, I’d
> suggest that you simply edit quantifyHAsubregions.sh (found in
> $FREESURFER_HOME/bin/) and replace these two lines:
>
> leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${
> suffix}.v20.txt"
>
> rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${
> suffix}.v20.txt"
>
>
>
> by:
>
>
>
> leftVolFile="$resultsDirectory/$subjectName/mri/lh.${prefix}Volumes-${
> suffix}.v20.txt"
>
> rightVolFile="$resultsDirectory/$subjectName/mri/rh.${prefix}Volumes-${
> suffix}.v20.txt"
>
>
>
> 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/
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Md. Mamun
> Al-Amin" <mdalaminba...@gmail.com>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Sunday, 17 September 2017 at 03:46
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation error
>
>
>
> Hi Eugenio
>
> Thanks for your attention.
>
> I solved this problem today. I found two JAVA versions in my macbook
> (Library/Java/JavaVirtualMachines). I think they were conflicting. So I
> deleted latest java folder.
>
> By the way, I have been trying to gather the volume analyzed from all
> subjects. However, it is not working.
>
> I used following command
> * quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/*
>
>
>
> However I found nothing in my CB_Long directory.
>
> Would you please help me solving this issue?
>
>
>
>
>
>
> On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> Dear MMAA,
>
> That looks like a runtime error. Did you have any problems with version
> 6.0?
>
> 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/
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Md. Mamun
> Al-Amin" <mdalaminba...@gmail.com>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Friday, 15 September 2017 at 00:54
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *[Freesurfer] Hippocampal subfield segmentation error
>
>
>
> Dear Experts
>
> I have been experiencing a problem while running the following command
>
>
>
> *segmentHA_T1.sh subject_name*
>
> The program exits with the following error
>
>
>
> "MATLAB is exiting because of fatal error
> /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
> line 39: 660 Killed: 9 "${exe_dir}"/segmentSubjectT1_
> autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
> $args"
>
> The log file is attached herewith.
>
> I have reinstalled Matlab R2012 runtime. However, still I am experiencing
> same problem.
>
>
> Looking for a solution.
>
> I would appreciate your suggestion.
>
>
>
> --
>
>
>
> 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.
>
>
>
>
> --
>
>
>
> Kin
Re: [Freesurfer] Hippocampal subfield segmentation error
Hi Eugenio
Thanks for your attention.
I solved this problem today. I found two JAVA versions in my macbook
(Library/Java/JavaVirtualMachines). I think they were conflicting. So I
deleted latest java folder.
By the way, I have been trying to gather the volume analyzed from all
subjects. However, it is not working.
I used following command
*quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/*
However I found nothing in my CB_Long directory.
Would you please help me solving this issue?
On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> Dear MMAA,
>
> That looks like a runtime error. Did you have any problems with version
> 6.0?
>
> 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/
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Md. Mamun
> Al-Amin" <mdalaminba...@gmail.com>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Friday, 15 September 2017 at 00:54
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *[Freesurfer] Hippocampal subfield segmentation error
>
>
>
> Dear Experts
>
> I have been experiencing a problem while running the following command
>
>
>
> *segmentHA_T1.sh subject_name*
>
> The program exits with the following error
>
>
>
> "MATLAB is exiting because of fatal error
> /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
> line 39: 660 Killed: 9 "${exe_dir}"/segmentSubjectT1_
> autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
> $args"
>
> The log file is attached herewith.
>
> I have reinstalled Matlab R2012 runtime. However, still I am experiencing
> same problem.
>
>
> Looking for a solution.
>
> I would appreciate your suggestion.
>
>
>
> --
>
>
>
> Kind regards
>
>
>
> Md. Mamun Al-Amin
>
> --
>
> PhD Candidate, Queensland Brain Institute
>
> Building 79, St Lucia QLD 4072
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
--
Kind regards
Md. Mamun Al-Amin
--
PhD Candidate, Queensland Brain Institute
Building 79, St Lucia QLD 4072
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Hippocampal subfield segmentation error
Dear Experts
I have been experiencing a problem while running the following command
*segmentHA_T1.sh subject_name*
The program exits with the following error
"MATLAB is exiting because of fatal error
/Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 39: 660 Killed: 9
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args"
The log file is attached herewith.
I have reinstalled Matlab R2012 runtime. However, still I am experiencing
same problem.
Looking for a solution.
I would appreciate your suggestion.
--
Kind regards
Md. Mamun Al-Amin
--
PhD Candidate, Queensland Brain Institute
Building 79, St Lucia QLD 4072
hippocampal-subfields-T1.log
Description: Binary data
___
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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.
Re: [Freesurfer] Extract coordinates from .mgh file
Hi I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. This file is stored in the mri folder. Would you please help me in this regards? kind regards Mamun On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug <redwanmaat...@gmail.com> wrote: > Hi Doug, > > Thank you for your reply, > I have used the tool *surf_cluster* to have the MNI coordinates. > Is it a good alternative to *mri_cor2label *? > > Thank you very much, > Regards, > Redwan > > On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> mri_cor2label with extract the coordinates into a label file. The >> coordinates will be in "tkregisterRAS". What coordinate system do you >> want? See >> >> See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems >> >> >> On 07/25/2017 07:32 PM, Redwan Maatoug wrote: >> > Hi experts, >> > >> > I just want to know a way to extract the coordinates from a ROI mgh >> file. >> > >> > I know that I can load the file with tksurfer but I have 100 .mgh >> > files so if I could run a command line to have the coordinates in a >> > .txt file or in a .m it would be helpful. >> > >> > Thank you, >> > Redwan >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> 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 ___ 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.
Re: [Freesurfer] Error in hippocampal subfield segmentation
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.igles...@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 <mdalaminba...@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.igles...@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 <mdalaminba...@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 = RBX = 00010331 >> RCX = 0006 RDX = 000103313a00 >> RSP = 00010fc39e80 RBP = 00d0 >> RSI = RDI = 0005 >> >>R8 = R9 = 000110323852 >> R10 = 72d27480 R11 = 72d274e0 >> R12 = 0005 R13 = 1c004121 >> R14 = 0246 R15 = 000110500160 >> >> RIP = 72d27b98 RFL = 72d27b60 >> >>CS = 00010f91fd54 FS = 72d27360 GS = 0005 >> >> Stack Trace (from fault): >> [ 0] 0x000101e61e46 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422 >> _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150 >> [ 1] 0x000101e62af1 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665 >> fl_diag_terminate+000321 >> [ 2] 0x000101e64c34 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180 >> _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100 >> [ 3] 0x000105ed825e >> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998 >> mnTrapCtrlc+000254 >> [ 4] 0x000105ed9d24 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852 >> _Z32mnRunPathDependentInitializationv+003492 >> [ 5] 0x000105eda13d >> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901 >> _Z32mnRunPathDependentInitializationv+004541 >> [ 6] 0x000105eda7f5 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621 >> _Z32mnRunPathDependentInitializationv+006261 >> [ 7] 0x000105eda945 >> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957 >> mnFatalSignalHandler+000149 >> [ 8] 0x7fffa5b60b3a >> /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+26 &g
Re: [Freesurfer] Error in hippocampal subfield segmentation
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.igles...@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 <mdalaminba...@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 = RBX = 00010331
> RCX = 0006 RDX = 000103313a00
> RSP = 00010fc39e80 RBP = 00d0
> RSI = RDI = 0005
>
>R8 = R9 = 000110323852
> R10 = 72d27480 R11 = 72d274e0
> R12 = 0005 R13 = 1c004121
> R14 = 0246 R15 = 000110500160
>
> RIP = 72d27b98 RFL = 72d27b60
>
>CS = 00010f91fd54 FS = 72d27360 GS = 0005
>
> Stack Trace (from fault):
> [ 0] 0x000101e61e46
> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422
> _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150
> [ 1] 0x000101e62af1
> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665
> fl_diag_terminate+000321
> [ 2] 0x000101e64c34
> /Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180
> _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100
> [ 3] 0x000105ed825e
> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998
> mnTrapCtrlc+000254
> [ 4] 0x000105ed9d24
> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852
> _Z32mnRunPathDependentInitializationv+003492
> [ 5] 0x000105eda13d
> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901
> _Z32mnRunPathDependentInitializationv+004541
> [ 6] 0x000105eda7f5
> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621
> _Z32mnRunPathDependentInitializationv+006261
> [ 7] 0x000105eda945
> /Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957
> mnFatalSignalHandler+000149
> [ 8] 0x7fffa5b60b3a
> /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+26
> [ 9] 0x0004
> /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] Error in hippocampal subfield segmentation
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 = RBX = 00010331
RCX = 0006 RDX = 000103313a00
RSP = 00010fc39e80 RBP = 00d0
RSI = RDI = 0005
R8 = R9 = 000110323852
R10 = 72d27480 R11 = 72d274e0
R12 = 0005 R13 = 1c004121
R14 = 0246 R15 = 000110500160
RIP = 72d27b98 RFL = 72d27b60
CS = 00010f91fd54 FS = 72d27360 GS = 0005
Stack Trace (from fault):
[ 0] 0x000101e61e46
/Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00036422
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000150
[ 1] 0x000101e62af1
/Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00039665
fl_diag_terminate+000321
[ 2] 0x000101e64c34
/Applications/freesurfer/MCRv80/bin/maci64/libmwfl.dylib+00048180
_ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000100
[ 3] 0x000105ed825e
/Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00315998
mnTrapCtrlc+000254
[ 4] 0x000105ed9d24
/Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00322852
_Z32mnRunPathDependentInitializationv+003492
[ 5] 0x000105eda13d
/Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00323901
_Z32mnRunPathDependentInitializationv+004541
[ 6] 0x000105eda7f5
/Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325621
_Z32mnRunPathDependentInitializationv+006261
[ 7] 0x000105eda945
/Applications/freesurfer/MCRv80/bin/maci64/libmwmcr.dylib+00325957
mnFatalSignalHandler+000149
[ 8] 0x7fffa5b60b3a
/usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+26
[ 9] 0x0004
/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
___
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