Dear all, our expert developer Zeke Kaufman figured out what the problem was. We have now fixed the Linux version; the MAC version will hopefully be ready as well in a couple of days. I have also fixed other bugs (including the problem that caused the code to get stuck every once in a while). You can downloaded the latest development version from our website. Thanks everyone for your feedback. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 8 Jul 2016, at 12:14, Iglesias, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/

On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis <RPEREACAMARGO@mgh.harvard.edumailto:RPEREACAMARGO@mgh.harvard.edu> wrote:

Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.

Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is:

Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash).

Thanks in advance for your help, Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.

--- Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo@mgh.harvard.edumailto:rpereacamargo@mgh.harvard.edu

This is a message from the E-Mail Virus Protection System at UCL ----------------------------------------------------------------------

The original e-mail attachment (recon-all.cmd) is on the list of unacceptable attachments for UCL and has been replaced by this warning message. This constraint is in place to protect users from viruses and other malware.

If you think this attachment is a legitimate file and you wish to receive it, please ask the sender to rename the file extension (eg rename file.exe to file.ex_) and resend it to avoid this constraint. On receiving the file you will have to save it and rename it back to its original extension.

Reference: 1bLDxs-0003ZW-3F

-- UCL E-mail Virus Protection System Servicedesk@ucl.ac.ukmailto:Servicedesk@ucl.ac.uk Internal phone: 25000

<hippocampal-subfields-T1T2.log><recon-all.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.

_______________________________________________ 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.

Hi,

I downloaded the new freesurfer development version and I still have the same problem when running the hippocampal-subfields

"Invalid MEX-file '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared object file: No such file or directory Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)

MATLAB:invalidMEXFile".

Does anyone have any idea about a solution ?

Cheers, Pierre

On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

And thanks to Zeke, of course ;-)

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 13 Jul 2016, at 11:19, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

Dear all, our expert developer Zeke Kaufman figured out what the problem was. We have now fixed the Linux version; the MAC version will hopefully be ready as well in a couple of days. I have also fixed other bugs (including the problem that caused the code to get stuck every once in a while). You can downloaded the latest development version from our website. Thanks everyone for your feedback. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 8 Jul 2016, at 12:14, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < RPEREACAMARGO@mgh.harvard.edu> wrote:

*Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.* Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is:

Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash).

Thanks in advance for your help, Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.

---

Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo@mgh.harvard.edu

This is a message from the E-Mail Virus Protection System at UCL

The original e-mail attachment (recon-all.cmd) is on the list of unacceptable attachments for UCL and has been replaced by this warning message. This constraint is in place to protect users from viruses and other malware.

If you think this attachment is a legitimate file and you wish to receive it, please ask the sender to rename the file extension (eg rename file.exe to file.ex_) and resend it to avoid this constraint. On receiving the file you will have to save it and rename it back to its original extension.

Reference: 1bLDxs-0003ZW-3F

-- UCL E-mail Virus Protection System Servicedesk@ucl.ac.uk Internal phone: 25000

<hippocampal-subfields-T1T2.log><recon-all.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.

---

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.

ok thanks a lot for the quick answer.

let me know when it works. our mri voxel size is 1 mm isotropic. (if it changes anything, I am working on ubuntu 14.04).

Cheers, Pierre

On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

Thanks a lot, Pierre. I’ll get this sorted out as soon as possible. I’m in the process of modifying the module so it supports data with resolution >1mm, and also incorporating the longitudinal segmentation method described in https://doi.org/10.1016/j.neuroimage.2016.07.020 Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 20 Jul 2016, at 09:57, pierre deman deman.pierre@gmail.com wrote:

Hi,

I downloaded the new freesurfer development version and I still have the same problem when running the hippocampal-subfields

"Invalid MEX-file '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared object file: No such file or directory Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)

MATLAB:invalidMEXFile".

Does anyone have any idea about a solution ?

Cheers, Pierre

On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

...

And thanks to Zeke, of course ;-)

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 13 Jul 2016, at 11:19, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

Dear all, our expert developer Zeke Kaufman figured out what the problem was. We have now fixed the Linux version; the MAC version will hopefully be ready as well in a couple of days. I have also fixed other bugs (including the problem that caused the code to get stuck every once in a while). You can downloaded the latest development version from our website. Thanks everyone for your feedback. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 8 Jul 2016, at 12:14, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < RPEREACAMARGO@mgh.harvard.edu> wrote:

*Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.* Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is:

Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash).

Thanks in advance for your help, Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.

---

Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo@mgh.harvard.edu

This is a message from the E-Mail Virus Protection System at UCL

The original e-mail attachment (recon-all.cmd) is on the list of unacceptable attachments for UCL and has been replaced by this warning message. This constraint is in place to protect users from viruses and other malware.

If you think this attachment is a legitimate file and you wish to receive it, please ask the sender to rename the file extension (eg rename file.exe to file.ex_) and resend it to avoid this constraint. On receiving the file you will have to save it and rename it back to its original extension.

Reference: 1bLDxs-0003ZW-3F

-- UCL E-mail Virus Protection System Servicedesk@ucl.ac.uk Internal phone: 25000

<hippocampal-subfields-T1T2.log><recon-all.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.

---

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.

-- DEMAN Pierre Mobile : +33 7 82 57 80 94 _______________________________________________ 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.