Dear Lauri, Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so the left model was not successfully flipped to create the right model – which is why your right hippocampus appears flipped. Andrew: any ideas on how to fix this? Cheers, /Eugenio PS: the dev version does not depend on this executable anymore

Hi Lauri,

This error is occurring because the libstdc++.so.6 library included with the linked matlab is older than the version shipped with centos7. While I think about the best way to resolve this, setting the following environment variable before running recon-all should clear everything up for now:

export LD_PRELOAD=/usr/lib64/libstdc++.so.6 # (with bash)

or

setenv LD_PRELOAD /usr/lib64/libstdc++.so.6 # (with tcsh)

best Andrew

On Jan 11, 2018, at 2:43 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote:

I think this is related to a matlab incompatibility. Can I see a copy of the log? Andrew

On Jan 11, 2018, at 12:09 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

Dear Lauri, Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so the left model was not successfully flipped to create the right model – which is why your right hippocampus appears flipped. Andrew: any ideas on how to fix this? Cheers, /Eugenio PS: the dev version does not depend on this executable anymore

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

On 10/01/2018, 21:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of e.iglesias@ucl.ac.uk> wrote:

Dear Lauri, Would you mind sending me the log of the subfield segmentation? Cheers, /Eugenio

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

On 08/01/2018, 22:04, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tuominen, Lauri Johannes" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of LTUOMINEN@mgh.harvard.edu> wrote:

Dear Freesurfers, When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment an MNI152 template, the resulting segmentation of left hippocampus got flipped in left-right dimension. Otherwise the right hippocampus and other subcortical segmentations in the aseg-file look fine. I encountered a similar problem when I tried to segment a T1 acquired at 7T. I run the command both locally and then on launchpad. Would you know how to fix this?

Thanks so much for your advice! Lauri Tuominen _______________________________________________ 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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer