External Email - Use Caution

I was thinking it could be a corrupt MCR cache. Could you please:

a) Delete /tmp/MCR* directories

b) Make sure you've got enough space in /tmp/

Cheers,

/Eugenio

Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sean Ma tehsheng@umich.edu Sent: Tuesday, July 3, 2018 1:43:18 AM To: Freesurfer support list Cc: Hoopes, Andrew Subject: Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

External Email - Use Caution

Hi Eugenio,

I’ve followed the wiki and installed it based on the instructions. My server runs on RHEL7.

Best,

Sean

On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

That’s rather ugly.

Sean: did you install the runtime from the Mathworks website, or did you download / uncompress following the instrucitons in the wiki?

Andrew: any ideas?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sean Ma <tehsheng@umich.edumailto:tehsheng@umich.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 2 July 2018 at 20:33 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

External Email - Use Caution

Hi Eugenio,

I'd like to report a Matlab runtime Java error when running the Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful completion of `recon-all`. Matlab 2014b runtime has been successfully expanded at /MCRv84.

The error I've encountered follows. Any suggestions on how I can overcome this error?

Thanks for your pointers!

Best,

Sean Ma

University of Michigan

==================================

[tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712

#--------------------------------------------

#@# Hippocampal Subfields processing (T1) left Mon Jul 2 15:16:41 EDT 2018

------------------------------------------

Setting up environment variables

---

LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64:

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)

@#@FSTIME 2018:07:02:15:16:41 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89

@#@FSLOADPOST 2018:07:02:15:17:13 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87

Linux b-fmri.eduhttp://b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Mon Jul 2 15:17:13 EDT 2018

For more details, see the log file /mnt/blab/Sean_Working/FS6results/b30002_02712/scripts/hippocampal-subfields-T1.log

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

External Email - Use Caution

Hi all, Not sure if this was resolved off-list or not, but I just ran into it myself and it turned out to be a permissions-related error in that the user didn't have read access to some of the required files in the Matlab runtime. Setting them appropriately resolved the issue.

Best, Niels

On Thu, Jul 5, 2018 at 9:37 PM Sean Ma tehsheng@umich.edu wrote:

    External Email - Use Caution

Hi Eugenio,

Thanks for the tip.

I've deleted the /MCR* folder in /tmp and made sure I had enough space in /tmp - 9GB.

Unfortunately, the same error message still exists.

Let me know if I could further send any debugging logs to help isolate this issue.

Thanks for your help!

Best,

Sean University of Michigan

On Tue, Jul 3, 2018 at 5:59 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

...

    External Email - Use Caution

I was thinking it could be a corrupt MCR cache. Could you please:

a) Delete /tmp/MCR* directories

b) Make sure you've got enough space in /tmp/

Cheers,

/Eugenio

Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sean Ma < tehsheng@umich.edu> *Sent:* Tuesday, July 3, 2018 1:43:18 AM *To:* Freesurfer support list *Cc:* Hoopes, Andrew *Subject:* Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

    External Email - Use Caution

Hi Eugenio,

I’ve followed the wiki and installed it based on the instructions. My server runs on RHEL7.

Best,

Sean

On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

    External Email - Use Caution

That’s rather ugly.

Sean: did you install the runtime from the Mathworks website, or did you download / uncompress following the instrucitons in the wiki?

Andrew: any ideas?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sean Ma < tehsheng@umich.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, 2 July 2018 at 20:33 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

•    External Email - Use Caution        *
  
  

Hi Eugenio,

I'd like to report a Matlab runtime Java error when running the Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful completion of `recon-all`. Matlab 2014b runtime has been successfully expanded at /MCRv84.

The error I've encountered follows. Any suggestions on how I can overcome this error?

Thanks for your pointers!

Best,

Sean Ma

University of Michigan

==================================

[tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712

#--------------------------------------------

#@# Hippocampal Subfields processing (T1) left Mon Jul 2 15:16:41 EDT 2018

---

Setting up environment variables

---

LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64:

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

    at

com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

    at

com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

    at

com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

    at

com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

    at

com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)

@#@FSTIME 2018:07:02:15:16:41 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89

@#@FSLOADPOST 2018:07:02:15:17:13 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87

Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Mon Jul 2 15:17:13 EDT 2018

For more details, see the log file /mnt/blab/Sean_Working/FS6results/b30002_02712/scripts/hippocampal-subfields-T1.log

---

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.

---

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.