I tried that. but didn't work.

Cheers, Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio e.iglesias@ucl.ac.uk wrote:

Hi everyone, you need to install the Matlab 2012b runtime as explained in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio

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

On 27 Jun 2016, at 15:16, pierre deman deman.pierre@gmail.com wrote:

Hello,

I have similar problem. " "Error:Cannot find CTF archive

/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" the file is here but when I try to execute it, it's always missing some library (libmwi18n.so for example, it was missing others before that I added on my computer, but it never ends....) I am on ubuntu 14.04. I thought that the problem is linked to the matlab runtime. I installed the 2012b. I tried newer version. installed again the 2012b.

Regards, Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon < Permesh.Dhillon@nottingham.ac.uk> wrote:

...

Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week.

I’d ve grateful if you could assist me with the issue above.

Many thanks Permesh

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

---

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.

I could finally look into this. It is indeed weird. The CTF is indeed embedded in the executable… Zeke/Nick, can you shed some light on this? Cheers, Eugenio

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

On 27 Jun 2016, at 15:43, Iglesias, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

Hi Pierre, Due to some technical problems, it might take me a couple of days to figure out what’s going on. But it definitely sounds funny that it is asking for the CTF, since this is supposed to be embedded in the executable… I’ll get back to you as soon as possible. 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 27 Jun 2016, at 15:32, pierre deman <deman.pierre@gmail.commailto:deman.pierre@gmail.com> wrote:

I tried that. but didn't work.

Cheers, Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote: Hi everyone, you need to install the Matlab 2012b runtime as explained in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime 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 27 Jun 2016, at 15:16, pierre deman <deman.pierre@gmail.commailto:deman.pierre@gmail.com> wrote:

Hello,

I have similar problem. " "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" the file is here but when I try to execute it, it's always missing some library (libmwi18n.so for example, it was missing others before that I added on my computer, but it never ends....) I am on ubuntu 14.04. I thought that the problem is linked to the matlab runtime. I installed the 2012b. I tried newer version. installed again the 2012b.

Regards, Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <Permesh.Dhillon@nottingham.ac.ukmailto:Permesh.Dhillon@nottingham.ac.uk> wrote: Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week.

I’d ve grateful if you could assist me with the issue above.

Many thanks Permesh

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

_______________________________________________ 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.

-- DEMAN Pierre Mobile : +33 7 82 57 80 94tel:%2B33%207%2082%2057%2080%2094 _______________________________________________ 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.

-- DEMAN Pierre Mobile : +33 7 82 57 80 94 _______________________________________________ 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 still have a problem as well with the subfields segmentation (ubuntu 14.04, with the files .ctf)

Cheers, Pierre Hello FreeSurfer Experts,

I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week.

I’d ve grateful if you could assist me with the issue above.

Many thanks Permesh

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

_______________________________________________ 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.