Re: [HCP-Users] Perl issues with Freesurfer5.3
Do you think a fix in the meantime until the hi-res v6.0 tools are availablemay be possible by making a V6.0HCP where the 5.3 tools relevant to the highres pial and highres white could be inserted into 6.0I understand this probably would require things like mris_make_surfaces etc to have their image calls changed to 6.0 terms like white.preaparc etc and recompiled from source code but do you think this would fix 6.0 for the pipelinesIs it known what change from 5.3 to 6.0 caused the issues? On Mon, Nov 19, 2018 at 6:26 AM Glasser, Matthew wrote: > This is still being actively worked on. Unfortunately FS6.0 doesn’t work > well for highres T1w and T2w (we will be using FreeSurfer’s own > functionalities for this in the future once they are working). Once we > have something ready and vetted, we will announce it and make it available > to everyone. > > Perhaps you could see if the FS6.0 MNI tools could be put in the FS5.3 > distribution and work okay as a workaround. > > Matt. > > From: on behalf of Michael > Sughrue > Date: Sunday, November 18, 2018 at 12:44 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Perl issues with Freesurfer5.3 > > I have been working on running the pipelines on a new computer which runs > on ubuntu18 and when running Freesurfer5.3HCP it crashes like described in > this post > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045407.html> > > > > which seems to be a known incompatibility with freesurfer5.3 involving > newer versions of perl playing badly with version 5.3 and which has been > fixed in version 6.0 (I assume it has because 6.0 seems to > work)…..According to Perlbrew this version of Ubuntu can install back to > perlv5.4 and I spent several hours trying to force install various versions > of perl which predate the glitch (5.0.1, 5.0.3 etc) and none of them are > functional on the new ubuntu and this does not fix the problem > > > > Freesurfer 6.0 runs basically fine through the system with some basic > editing of the freesurferpipeline.sh except for the obvious compatibility > problem with mri_make_surfaces in the high res white part which you guys > are aware of…obviously I can push this through by editing the high res > steps out but this causes a chain effect with making myelin maps, and then > steps which require that step for fMRI processing etc > > > > Is there a solution for this which doesn’t involve changing operating > systems…do versions of the highres white and highres pial scripts exist > which will work with V6.0 (even if not perfect) > > > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Perl issues with Freesurfer5.3
No that would not be a good fix. I would focus on working around the bug in 5.3 (e.g. by updating the MNI tools) or hopefully we will have a FS 6.0+ that works nearly as well as 5.3. Matt. From: Michael Sughrue mailto:sughru...@gmail.com>> Date: Sunday, November 18, 2018 at 6:41 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Perl issues with Freesurfer5.3 Do you think a fix in the meantime until the hi-res v6.0 tools are availablemay be possible by making a V6.0HCP where the 5.3 tools relevant to the highres pial and highres white could be inserted into 6.0I understand this probably would require things like mris_make_surfaces etc to have their image calls changed to 6.0 terms like white.preaparc etc and recompiled from source code but do you think this would fix 6.0 for the pipelinesIs it known what change from 5.3 to 6.0 caused the issues? On Mon, Nov 19, 2018 at 6:26 AM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: This is still being actively worked on. Unfortunately FS6.0 doesn’t work well for highres T1w and T2w (we will be using FreeSurfer’s own functionalities for this in the future once they are working). Once we have something ready and vetted, we will announce it and make it available to everyone. Perhaps you could see if the FS6.0 MNI tools could be put in the FS5.3 distribution and work okay as a workaround. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Michael Sughrue mailto:sughru...@gmail.com>> Date: Sunday, November 18, 2018 at 12:44 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Perl issues with Freesurfer5.3 I have been working on running the pipelines on a new computer which runs on ubuntu18 and when running Freesurfer5.3HCP it crashes like described in this post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045407.html> which seems to be a known incompatibility with freesurfer5.3 involving newer versions of perl playing badly with version 5.3 and which has been fixed in version 6.0 (I assume it has because 6.0 seems to work)…..According to Perlbrew this version of Ubuntu can install back to perlv5.4 and I spent several hours trying to force install various versions of perl which predate the glitch (5.0.1, 5.0.3 etc) and none of them are functional on the new ubuntu and this does not fix the problem Freesurfer 6.0 runs basically fine through the system with some basic editing of the freesurferpipeline.sh except for the obvious compatibility problem with mri_make_surfaces in the high res white part which you guys are aware of…obviously I can push this through by editing the high res steps out but this causes a chain effect with making myelin maps, and then steps which require that step for fMRI processing etc Is there a solution for this which doesn’t involve changing operating systems…do versions of the highres white and highres pial scripts exist which will work with V6.0 (even if not perfect) Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Perl issues with Freesurfer5.3
This is still being actively worked on. Unfortunately FS6.0 doesn’t work well for highres T1w and T2w (we will be using FreeSurfer’s own functionalities for this in the future once they are working). Once we have something ready and vetted, we will announce it and make it available to everyone. Perhaps you could see if the FS6.0 MNI tools could be put in the FS5.3 distribution and work okay as a workaround. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Michael Sughrue mailto:sughru...@gmail.com>> Date: Sunday, November 18, 2018 at 12:44 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Perl issues with Freesurfer5.3 I have been working on running the pipelines on a new computer which runs on ubuntu18 and when running Freesurfer5.3HCP it crashes like described in this post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045407.html> which seems to be a known incompatibility with freesurfer5.3 involving newer versions of perl playing badly with version 5.3 and which has been fixed in version 6.0 (I assume it has because 6.0 seems to work)…..According to Perlbrew this version of Ubuntu can install back to perlv5.4 and I spent several hours trying to force install various versions of perl which predate the glitch (5.0.1, 5.0.3 etc) and none of them are functional on the new ubuntu and this does not fix the problem Freesurfer 6.0 runs basically fine through the system with some basic editing of the freesurferpipeline.sh except for the obvious compatibility problem with mri_make_surfaces in the high res white part which you guys are aware of…obviously I can push this through by editing the high res steps out but this causes a chain effect with making myelin maps, and then steps which require that step for fMRI processing etc Is there a solution for this which doesn’t involve changing operating systems…do versions of the highres white and highres pial scripts exist which will work with V6.0 (even if not perfect) Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Perl issues with Freesurfer5.3
I have been working on running the pipelines on a new computer which runs on ubuntu18 and when running Freesurfer5.3HCP it crashes like described in this post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html which seems to be a known incompatibility with freesurfer5.3 involving newer versions of perl playing badly with version 5.3 and which has been fixed in version 6.0 (I assume it has because 6.0 seems to work)…..According to Perlbrew this version of Ubuntu can install back to perlv5.4 and I spent several hours trying to force install various versions of perl which predate the glitch (5.0.1, 5.0.3 etc) and none of them are functional on the new ubuntu and this does not fix the problem Freesurfer 6.0 runs basically fine through the system with some basic editing of the freesurferpipeline.sh except for the obvious compatibility problem with mri_make_surfaces in the high res white part which you guys are aware of…obviously I can push this through by editing the high res steps out but this causes a chain effect with making myelin maps, and then steps which require that step for fMRI processing etc Is there a solution for this which doesn’t involve changing operating systems…do versions of the highres white and highres pial scripts exist which will work with V6.0 (even if not perfect) Sent from Mail for Windows 10 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
