External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version worked just great! All the recon-all procedures were managed via Linux based computing cluster. (We never had any perturbations in the performance there; 1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We observer a strange thing: once the longitudal version reached some undefined number of subjects (30-50 jobs) it only produces the left hemisphere text file. The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the longitudal version given 3 time points of the observation.

Here are all log files from the long version: https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely, Nikita

On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us the log file of the hippocampal subfields (rather than of recon-all)? Cheers, /Eugenio

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.comhttp://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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 16:49 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution

HI

I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks Nikita _______________________________________________ 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.

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My apologies. Here is the long-hippocampal-subfields-T1.log https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD

On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

Thanks, Nikita. Can you please send us the file long-hippocampal-subfields-T1.log, which you can find under the base subject, for one of the failing cases? Cheers, /E

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.comhttp://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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 17:36 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version worked just great! All the recon-all procedures were managed via Linux based computing cluster. (We never had any perturbations in the performance there; 1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We observer a strange thing: once the longitudal version reached some undefined number of subjects (30-50 jobs) it only produces the left hemisphere text file. The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the longitudal version given 3 time points of the observation.

Here are all log files from the long version: https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely, Nikita

On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us the log file of the hippocampal subfields (rather than of recon-all)? Cheers, /Eugenio

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.comhttp://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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 16:49 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution HI

I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks Nikita _______________________________________________ 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.

_______________________________________________ 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

Thank you Eugenio, there were no error messages or any observations that may indicate the computing process experienced perturbations...

Nikita

On Jun 12, 2018, at 12:19, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution Uuuummm it seems it died unexpectedly, but there’s no error at the end of the log… are you sure that’s the complete file? If not: did you get any other message on the screen when you tried to run this? 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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 17:52 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution My apologies. Here is the long-hippocampal-subfields-T1.log https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD

On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

Thanks, Nikita. Can you please send us the file long-hippocampal-subfields-T1.log, which you can find under the base subject, for one of the failing cases? Cheers, /E

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.comhttp://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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 17:36 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version worked just great! All the recon-all procedures were managed via Linux based computing cluster. (We never had any perturbations in the performance there; 1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We observer a strange thing: once the longitudal version reached some undefined number of subjects (30-50 jobs) it only produces the left hemisphere text file. The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the longitudal version given 3 time points of the observation.

Here are all log files from the long version: https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely, Nikita

On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution

Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us the log file of the hippocampal subfields (rather than of recon-all)? Cheers, /Eugenio

-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.comhttp://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 Nikita Nogovitsyn <n.nogovitsyn@ucalgary.camailto:n.nogovitsyn@ucalgary.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 12 June 2018 at 16:49 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution HI

I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks Nikita _______________________________________________ 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.

_______________________________________________ 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.

_______________________________________________ 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.