segmentHA_T1.sh Error

List overview All Threads
Download

newer

older

ubuntu 20.4?

mri_watershed error: problem in...

Zachary Miller

21 Dec 2020 21 Dec '20

12:13 p.m.

External Email - Use Caution

Hello,

I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below.

Thank you, Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

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

Setting up environment variables

---

LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu University of Minnesota | umn.edu mill5076@umn.edu

Attachments:

attachment.html (text/html — 8.7 KB)

Show replies by date

Iglesias Gonzalez, Juan E.

21 Dec 21 Dec

12:42 p.m.

Hi Zach, Just to double check: your directory structure is: FStests/CDN0001_MSB/CDN0001 So the following directory: FStests/CDN0001_MSB/CDN0001/tmp exists and is writable? For example, this command: echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt will create the file: FStests/CDN0001_MSB/CDN0001/tmp/test.txt Cheers, 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 Zachary Miller mill5076@umn.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, December 21, 2020 at 12:14 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1.sh Error

External Email - Use Caution Hello,

Thank you, Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

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

Setting up environment variables

---

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

Zachary Miller

1:16 p.m.

New subject: segmentHA_T1.sh Error {Disarmed}

External Email - Use Caution

My directory structure is: FStests/CDN0001_MSB/CDN0001_10_7.1.1

The command echo Hello > FStests/CDN0001_MSB/CDN0001_10_7.1.1/tmp/test.txt does create test.txt in the tmp directory.

On Mon, Dec 21, 2020 at 11:43 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

...

Hi Zach,

Just to double check: your directory structure is:

FStests/CDN0001_MSB/CDN0001

So the following directory:

FStests/CDN0001_MSB/CDN0001/tmp

exists and is writable? For example, this command:

echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt

will create the file:

FStests/CDN0001_MSB/CDN0001/tmp/test.txt

Cheers,

Juan Eugenio Iglesias

Senior research fellow

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

http://secure-web.cisco.com/1SBWEcUoApMZs8bq9HMCxtpaV6K931cl2CvT4gy1zOHkugGx...

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zachary Miller mill5076@umn.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, December 21, 2020 at 12:14 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] segmentHA_T1.sh Error
   External Email - Use Caution        *
Hello,

I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below.

Thank you,

Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

Setting up environment variables

LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

--

Zachary Miller

Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu http://secure-web.cisco.com/1sz1OjDmLqXbn7QdcfQPSyVRpMWzjVeK8cvH2a4MYh2hG2Y3iLeIhIEkgnzntI3yZYCagi1FFxnF4exfBfm4jCfM0HiHS99i9uMcYaoQt1641hmLuwdjjYNAJZYm-WO1RbLKUNg_w1hvGXYxGcLZn1TnkdsmO3N9rDo7yNPgLhKgXE5udATYH_r5OqPMp4pY9KXelAaP7_IJcyDr7gJRXqLNMwPA5W8IRJYoShY-4XZL5yML3DwBN-SAtqVEWzw7NceUQQWYcqRyFCHb00QOTgg/http%3A%2F%2Fcehd.umn.edu

University of Minnesota | umn.edu http://secure-web.cisco.com/1CbIw_leTY7V-HIZSQ3DPCA9YQP-fo1yBfYmrMLo4VQnEsKUkXbXrGoYBIIf_QMd7Sksg37PoDUrEAdVUbeaoI82xjBfvkopbPVddsNF0qwg9KOm4QBqTLlFI6Gi4fgMUT5Vy5YRBxlSYNFHHFVMRCtaPCDRmvkDDezVdUU_vO5EV2XevV6AFh66x9Y6y_RH5bO4pHwvtDv3O1fYT-CkHbHhrw2RYsE_Qu3kQV75nr60CBgE9vxQRfyPAtiuOiVeAZdAhSq2vwvMZJHwT-xVaVg/http%3A%2F%2Fumn.edu

mill5076@umn.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rjhYE_DWGQhGXDnFoMwsSKsc69IcMr4ne8f24CsBhl5xql...

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu University of Minnesota | umn.edu mill5076@umn.edu

Iglesias Gonzalez, Juan E.

1:43 p.m.

New subject: segmentHA_T1.sh Error {Disarmed}

Thanks, Zach. May I ask you to try running the command with an absolute path for the subjects directory, please? Cheers, /Eugenio

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 Zachary Miller mill5076@umn.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, December 21, 2020 at 13:17 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentHA_T1.sh Error {Disarmed}

External Email - Use Caution My directory structure is: FStests/CDN0001_MSB/CDN0001_10_7.1.1

The command echo Hello > FStests/CDN0001_MSB/CDN0001_10_7.1.1/tmp/test.txt does create test.txt in the tmp directory.

On Mon, Dec 21, 2020 at 11:43 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Hi Zach, Just to double check: your directory structure is: FStests/CDN0001_MSB/CDN0001 So the following directory: FStests/CDN0001_MSB/CDN0001/tmp exists and is writable? For example, this command: echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt will create the file: FStests/CDN0001_MSB/CDN0001/tmp/test.txt Cheers, Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com http://secure-web.cisco.com/1SBWEcUoApMZs8bq9HMCxtpaV6K931cl2CvT4gy1zOHkugGxfbNxsMvSmHJ2vsCHMrtaOePASgCGLL8UrI1YT7l3-yp5APSOovtASvFuGlxIgEf8ijjlIbsWuaysX9_b5RG3jbFeT_77sP9caDU5j35lCc3u4N9gtYlSlI_hwag5yMEMkdkNYtp6w4fcOQYkpO8AThrfa8IqcpoBALS0FnsMeQvp-akSqHYXqhbaY32VzepuLIKXt1DtjXY6Wskf1V0VQWIBqy95DgfRAIBUl-Q/http%3A%2F%2Fwww.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zachary Miller <mill5076@umn.edumailto:mill5076@umn.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 21, 2020 at 12:14 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T1.sh Error

External Email - Use Caution Hello,

Thank you, Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

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

Setting up environment variables

---

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.eduhttp://secure-web.cisco.com/1sz1OjDmLqXbn7QdcfQPSyVRpMWzjVeK8cvH2a4MYh2hG2Y3iLeIhIEkgnzntI3yZYCagi1FFxnF4exfBfm4jCfM0HiHS99i9uMcYaoQt1641hmLuwdjjYNAJZYm-WO1RbLKUNg_w1hvGXYxGcLZn1TnkdsmO3N9rDo7yNPgLhKgXE5udATYH_r5OqPMp4pY9KXelAaP7_IJcyDr7gJRXqLNMwPA5W8IRJYoShY-4XZL5yML3DwBN-SAtqVEWzw7NceUQQWYcqRyFCHb00QOTgg/http%3A%2F%2Fcehd.umn.edu University of Minnesota | umn.eduhttp://secure-web.cisco.com/1CbIw_leTY7V-HIZSQ3DPCA9YQP-fo1yBfYmrMLo4VQnEsKUkXbXrGoYBIIf_QMd7Sksg37PoDUrEAdVUbeaoI82xjBfvkopbPVddsNF0qwg9KOm4QBqTLlFI6Gi4fgMUT5Vy5YRBxlSYNFHHFVMRCtaPCDRmvkDDezVdUU_vO5EV2XevV6AFh66x9Y6y_RH5bO4pHwvtDv3O1fYT-CkHbHhrw2RYsE_Qu3kQV75nr60CBgE9vxQRfyPAtiuOiVeAZdAhSq2vwvMZJHwT-xVaVg/http%3A%2F%2Fumn.edu mill5076@umn.edumailto:mill5076@umn.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1rjhYE_DWGQhGXDnFoMwsSKsc69IcMr4ne8f24CsBhl5xqlSb61-dhdi2ifSO7-_c1uAjmVChleL0eLw-Wp4vJGmZX-SgyUUps4cOOBNddxga2Hw9bXfAqRhCryAigIQjm53_0w1VAjqSysrGAvRxCpwTEIJaCkqTXWl_zm8_Cba8JtH-t1v7GwSe6LIwqt3sW2XGx2lADJNX1Lg4YntKTU8QWbHODD6MbTavbHzM5j8HcuYjkM_cePmDPfS7ZBUlpvsA73UnX4JOXkJO2pDDyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Zachary Miller

3:28 p.m.

New subject: segmentHA_T1.sh Error {Disarmed}

External Email - Use Caution

That did the trick, thank you!

On Mon, Dec 21, 2020 at 12:43 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

...

Thanks, Zach. May I ask you to try running the command with an absolute path for the subjects directory, please?

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

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

http://secure-web.cisco.com/1bRUKxXjytzl-yJaVkXunh__6KCeqv2CjEiNZh17y5cE47Nw...

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zachary Miller mill5076@umn.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, December 21, 2020 at 13:17 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] segmentHA_T1.sh Error {Disarmed}
   External Email - Use Caution        *
My directory structure is:

FStests/CDN0001_MSB/CDN0001_10_7.1.1

The command echo Hello > FStests/CDN0001_MSB/CDN0001_10_7.1.1/tmp/test.txt

does create test.txt in the tmp directory.

On Mon, Dec 21, 2020 at 11:43 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Hi Zach,

Just to double check: your directory structure is:

FStests/CDN0001_MSB/CDN0001

So the following directory:

FStests/CDN0001_MSB/CDN0001/tmp

exists and is writable? For example, this command:

echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt

will create the file:

FStests/CDN0001_MSB/CDN0001/tmp/test.txt

Cheers,

Juan Eugenio Iglesias

Senior research fellow

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

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1bRUKxXjytzl-yJaVkXunh__6KCeqv2CjEiNZh17y5cE47Nw... http://secure-web.cisco.com/1SBWEcUoApMZs8bq9HMCxtpaV6K931cl2CvT4gy1zOHkugGxfbNxsMvSmHJ2vsCHMrtaOePASgCGLL8UrI1YT7l3-yp5APSOovtASvFuGlxIgEf8ijjlIbsWuaysX9_b5RG3jbFeT_77sP9caDU5j35lCc3u4N9gtYlSlI_hwag5yMEMkdkNYtp6w4fcOQYkpO8AThrfa8IqcpoBALS0FnsMeQvp-akSqHYXqhbaY32VzepuLIKXt1DtjXY6Wskf1V0VQWIBqy95DgfRAIBUl-Q/http%3A%2F%2Fwww.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zachary Miller mill5076@umn.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, December 21, 2020 at 12:14 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] segmentHA_T1.sh Error
   External Email - Use Caution        *
Hello,

I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below.

Thank you,

Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

Setting up environment variables

LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

--

Zachary Miller

Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu http://secure-web.cisco.com/1sz1OjDmLqXbn7QdcfQPSyVRpMWzjVeK8cvH2a4MYh2hG2Y3iLeIhIEkgnzntI3yZYCagi1FFxnF4exfBfm4jCfM0HiHS99i9uMcYaoQt1641hmLuwdjjYNAJZYm-WO1RbLKUNg_w1hvGXYxGcLZn1TnkdsmO3N9rDo7yNPgLhKgXE5udATYH_r5OqPMp4pY9KXelAaP7_IJcyDr7gJRXqLNMwPA5W8IRJYoShY-4XZL5yML3DwBN-SAtqVEWzw7NceUQQWYcqRyFCHb00QOTgg/http%3A%2F%2Fcehd.umn.edu

University of Minnesota | umn.edu http://secure-web.cisco.com/1CbIw_leTY7V-HIZSQ3DPCA9YQP-fo1yBfYmrMLo4VQnEsKUkXbXrGoYBIIf_QMd7Sksg37PoDUrEAdVUbeaoI82xjBfvkopbPVddsNF0qwg9KOm4QBqTLlFI6Gi4fgMUT5Vy5YRBxlSYNFHHFVMRCtaPCDRmvkDDezVdUU_vO5EV2XevV6AFh66x9Y6y_RH5bO4pHwvtDv3O1fYT-CkHbHhrw2RYsE_Qu3kQV75nr60CBgE9vxQRfyPAtiuOiVeAZdAhSq2vwvMZJHwT-xVaVg/http%3A%2F%2Fumn.edu

mill5076@umn.edu

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-_LV09YJ66hEhQdIziW1cfKWGhmvS6LHC-9iVyy3Hv-J7E... https://secure-web.cisco.com/1rjhYE_DWGQhGXDnFoMwsSKsc69IcMr4ne8f24CsBhl5xqlSb61-dhdi2ifSO7-_c1uAjmVChleL0eLw-Wp4vJGmZX-SgyUUps4cOOBNddxga2Hw9bXfAqRhCryAigIQjm53_0w1VAjqSysrGAvRxCpwTEIJaCkqTXWl_zm8_Cba8JtH-t1v7GwSe6LIwqt3sW2XGx2lADJNX1Lg4YntKTU8QWbHODD6MbTavbHzM5j8HcuYjkM_cePmDPfS7ZBUlpvsA73UnX4JOXkJO2pDDyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

--

Zachary Miller

Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu http://secure-web.cisco.com/1AsXe39tc1H_lb-QkLGA8jzJf8wkzBVtzcrLBjJPkqZQMdituG2FCxEn-n-irEaJDU8mryKrmHV2l4wAIleBDvrZ8JcUxifPtRIyoS0Vog4-T3VF0svkft6irFYM2cHKcdxL5kk4up4rl8P7nKuc4aTKKTjW3ALP6B-gRBy3J0ZUo2Bi0mipFs1iF8tF6RFOcVPI2K0Wt-abOQZhzAAZKDG3YdG2NGkn_eL3Dq7p5yZ3m0XuetVTyNi_3cZMqRYEsqQm8P0WJpGhk6IOiAoWbdg/http%3A%2F%2Fcehd.umn.edu

University of Minnesota | umn.edu http://secure-web.cisco.com/1_7j0JlZMb5sCoJi9HOMkanSR6gQOBYR6iWjEwRhMJICB61vp5TkCpzlInjlkAKmHbLRJJNdjwFuIf-L4PnwBZQC3VGkU6kL1nsCClUYsydZ7igU6m9amyqVHFXdBv6Bgp0X2XwDH3btAaqyn8C0nJM41LxjfyG2qctEcv05CbCOraiMvzzPHZsla136I4PphsV8dEVOJVUOoyJ0w-TVCiVFWsHPjdgjhPy2-TjpF_Tb4oZjBOurYgu9l3rYTxYMgBGvxYBymG0KPuySxNkijyQ/http%3A%2F%2Fumn.edu

mill5076@umn.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-_LV09YJ66hEhQdIziW1cfKWGhmvS6LHC-9iVyy3Hv-J7E...

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu University of Minnesota | umn.edu mill5076@umn.edu

Iglesias Gonzalez, Juan E.

8:10 p.m.

New subject: segmentHA_T1.sh Error {Disarmed}

Thank you for bearing with us. I thought this had been sorted in the previous version; my apologies.

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 Zachary Miller mill5076@umn.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, December 21, 2020 at 15:30 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentHA_T1.sh Error {Disarmed}

External Email - Use Caution That did the trick, thank you!

On Mon, Dec 21, 2020 at 12:43 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Thanks, Zach. May I ask you to try running the command with an absolute path for the subjects directory, please? Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com http://secure-web.cisco.com/1bRUKxXjytzl-yJaVkXunh__6KCeqv2CjEiNZh17y5cE47Nw-MNFcYTg9rnzQeMSxNpPJkZSA8GkgfYKVNqoaQReUwPI8hw0ttR2d_lXuJNWIf9Lbio2SA5flEKbiJ-sPW8GPQxBj1ccjy1xfNsM475RMbpWTzgeP1Uy_kMvcbrrjTyCmQ4xnjvhFJM6YdD0cxNPHWNmo2RVDLauXEIIaewMSpDbBuih52fK1eAkUewxG9x0t-3M63dSQzf8_xYieW6e4N2nEEyDvdeAN5iaO9w/http%3A%2F%2Fwww.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zachary Miller <mill5076@umn.edumailto:mill5076@umn.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 21, 2020 at 13:17 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] segmentHA_T1.sh Error {Disarmed}

External Email - Use Caution My directory structure is: FStests/CDN0001_MSB/CDN0001_10_7.1.1

The command echo Hello > FStests/CDN0001_MSB/CDN0001_10_7.1.1/tmp/test.txt does create test.txt in the tmp directory.

External Email - Use Caution Hello,

Thank you, Zach

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

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

Setting up environment variables

---

Registering imageDump.mgz to hippocampal mask from ASEG

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.eduhttp://secure-web.cisco.com/1AsXe39tc1H_lb-QkLGA8jzJf8wkzBVtzcrLBjJPkqZQMdituG2FCxEn-n-irEaJDU8mryKrmHV2l4wAIleBDvrZ8JcUxifPtRIyoS0Vog4-T3VF0svkft6irFYM2cHKcdxL5kk4up4rl8P7nKuc4aTKKTjW3ALP6B-gRBy3J0ZUo2Bi0mipFs1iF8tF6RFOcVPI2K0Wt-abOQZhzAAZKDG3YdG2NGkn_eL3Dq7p5yZ3m0XuetVTyNi_3cZMqRYEsqQm8P0WJpGhk6IOiAoWbdg/http%3A%2F%2Fcehd.umn.edu University of Minnesota | umn.eduhttp://secure-web.cisco.com/1_7j0JlZMb5sCoJi9HOMkanSR6gQOBYR6iWjEwRhMJICB61vp5TkCpzlInjlkAKmHbLRJJNdjwFuIf-L4PnwBZQC3VGkU6kL1nsCClUYsydZ7igU6m9amyqVHFXdBv6Bgp0X2XwDH3btAaqyn8C0nJM41LxjfyG2qctEcv05CbCOraiMvzzPHZsla136I4PphsV8dEVOJVUOoyJ0w-TVCiVFWsHPjdgjhPy2-TjpF_Tb4oZjBOurYgu9l3rYTxYMgBGvxYBymG0KPuySxNkijyQ/http%3A%2F%2Fumn.edu mill5076@umn.edumailto:mill5076@umn.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1-_LV09YJ66hEhQdIziW1cfKWGhmvS6LHC-9iVyy3Hv-J7EtxuIbyMAxcc4jX-e19S3oMsivHVq8k58ZeZOIAGm2P-pjZlkN4bFrkr2wGDslmsFkX_wCGL6ql87O6v63290xNaT11e0e_swsXJvk6ixQmsqHqd7e1eu0YwEoq4IOIUyFh8DqZBZ5kviq4Ipp16SxXaqJ_Tzq3dM9IARz9eq8gTvFXpry3xU6TdW8f9QAqc9e45iXl7QJafwznxTTVYSLi5_cDNN8HavXmN5nbYg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

-- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.eduhttp://secure-web.cisco.com/1MRVKK6LgHw57RZ5vTJ0pRh_z8XtarW-F434WKfEsgk5Z9axG1El-kzg5DGyHmNsdX3RY_FL2k1ekV6NJanLF75xettb7o7JZbgr-8cPsNEMdNUN8RTtuSHbEGqgLUfb8xD-Bl5hgTAPKoYwrCQMcsxNmqQu7ZWLOeHtfVlF2CDdxqGnj0Uv3Ff4TmK5q8m-3_AVzkX7lv0qLeOj0IomQ2uKRCwwphd3YOwvF2HRwPQV_eiR9WXWyLNZYdMJ7FANZknpq7TGxjx2prztth_bS1g/http%3A%2F%2Fcehd.umn.edu University of Minnesota | umn.eduhttp://secure-web.cisco.com/11PT-l-hEdeFIL2J9sbsZH_H8u19d2Xck4Sq6o-EPC7s5ejhlEew67EGs-tWL1VZ2cP1uNt0FRvUK6diTylaBb3b1ro6zs6VhoCIyq8R_FME6HjvO3_uj8NAfgqdAKRm-SvYMv1yIfVNgGtqCV6ZPja6bLyFvYBw0G310Uc_TpLK7meirS_bLCpRX0K3WmSvEgdnCuts9miktTBMaXrG5PeenICRwN1VHWBNb12x7m2mbH99J11ln7aPdaRTGXNhckz1XOIDqTKee1ax2pRwDdw/http%3A%2F%2Fumn.edu mill5076@umn.edumailto:mill5076@umn.edu

1989

Age (days ago)

1990

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

5 comments

2 participants

tags (0)

participants (2)

Iglesias Gonzalez, Juan E.
Zachary Miller