Bummer! Andrew, any ideas on this? Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Olamide Abiose oabiose@stanford.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 10 October 2019 at 15:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

External Email - Use Caution Thank you so much for your quick response. I saw this link and mentioned this to my server administrator, but he seemed to disagree that that was the source of the issue. There were definitely permissions issues when he first downloaded Matlab R2014b onto the server, but I think they've been resolved (I no longer have trouble accessing files and subdirectories within the MCRv84 folder). That being said, I haven't been able to find "checkRequiredMCRProducts," " deployrc," or "matlabrc," and I don't know where to begin to look. Please let me know if you have any suggestions! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, October 10, 2019 3:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

Dear Ola,

This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem.

https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...

Can you please double check this is not your case?

Cheers,

/E

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Olamide Abiose oabiose@stanford.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 10 October 2019 at 14:29 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issues with segmentHA_T1.sh command

External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated!

Thank you very much.

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

#@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019

/usr/bin/time -o /dev/stdout

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01

run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0

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

Setting up environment variables

---

LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::

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)

Command exited with non-zero status 255

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01

@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90

Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

Unfortunately, I have no idea. It might be worth contacting matlab support over this. It seems like others (non-freesurfer) have had this issue, but there isn't much out there on how to resolve it. Andrew

________________________________________ From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, October 10, 2019 3:33 PM To: Freesurfer support list Cc: Hoopes, Andrew Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

Bummer! Andrew, any ideas on this? Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Olamide Abiose oabiose@stanford.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 10 October 2019 at 15:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

External Email - Use Caution Thank you so much for your quick response. I saw this link and mentioned this to my server administrator, but he seemed to disagree that that was the source of the issue. There were definitely permissions issues when he first downloaded Matlab R2014b onto the server, but I think they've been resolved (I no longer have trouble accessing files and subdirectories within the MCRv84 folder). That being said, I haven't been able to find "checkRequiredMCRProducts," " deployrc," or "matlabrc," and I don't know where to begin to look. Please let me know if you have any suggestions! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, October 10, 2019 3:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

Dear Ola,

This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem.

https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...

Can you please double check this is not your case?

Cheers,

/E

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Olamide Abiose oabiose@stanford.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 10 October 2019 at 14:29 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issues with segmentHA_T1.sh command

External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated!

Thank you very much.

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

#@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019

/usr/bin/time -o /dev/stdout

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01

run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0

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

Setting up environment variables

---

LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::

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)

Command exited with non-zero status 255

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01

@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90

Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019