Hello Yaroslav,
Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed. Ive update the wiki page:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out.
-Zeke
On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
Gotcha, thanks!
On February 18, 2016 3:27:21 PM EST, Z K zkaufman@nmr.mgh.harvard.edu wrote:
I would be infinitely grateful if freesurfer could build natively on
Debian
stable! ;) Thanks for trying. In my case I am trying the build
under jessie
chroot (using schroot helper), so I could quickly setup/enter such
environment
while maintaining user/directory. I will do the same now for 14.04.
If you
would like more -- let me know I could give a bit more detailed instructions.
I have a debian jessie system just setup, but I have a high priority project due Monday, so I would be able to begin determining the exact build procedure on Debian jessie until beginning of next week. It is something I have been meaning to do so I plan on getting to it. If you dont hear from me by Tuesday/Wedensday feel free to shoot me an email for an update. Thanks.
-Zeke
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 have been able to build the FS GUI tools succesfully on Ubuntu in the past... Admittedly this was a long time ago (pre 14.04 days). I can dig through my notes and see if they are still applicable. We no longer have any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose in a few weeks will be superseded by 16.04's release.
On 2/19/16 12:45 , Z K wrote:
Hello Yaroslav,
Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed. Ive update the wiki page:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out.
-Zeke
On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
Gotcha, thanks!
On February 18, 2016 3:27:21 PM EST, Z K zkaufman@nmr.mgh.harvard.edu wrote:
I would be infinitely grateful if freesurfer could build natively on
Debian
stable! ;) Thanks for trying. In my case I am trying the build
under jessie
chroot (using schroot helper), so I could quickly setup/enter such
environment
while maintaining user/directory. I will do the same now for 14.04.
If you
would like more -- let me know I could give a bit more detailed instructions.
I have a debian jessie system just setup, but I have a high priority project due Monday, so I would be able to begin determining the exact build procedure on Debian jessie until beginning of next week. It is something I have been meaning to do so I plan on getting to it. If you dont hear from me by Tuesday/Wedensday feel free to shoot me an email for an update. Thanks.
-Zeke
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
Ive discovered that if you add the following line to the freeview/Makefile.am file then it will build succcessfully.
freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -freeview_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) +freeview_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) \ + -Wl,--allow-multiple-definition freeview_LDADD = $(QT_LIBS) \ $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ $(top_builddir)/vtkfsio/libvtkfsio.a \
Turns out the issue is with the build of LAPACK provided by Ubuntu, as it contains a duplicate function. (https://cmake.org/Bug/view.php?id=12912)
I will be committing the change and pushing to the git repo after some testing, probably later this evening.
-Zeke
On 02/19/2016 02:29 PM, Rudolph Pienaar wrote:
I have been able to build the FS GUI tools succesfully on Ubuntu in the past... Admittedly this was a long time ago (pre 14.04 days). I can dig through my notes and see if they are still applicable. We no longer have any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose in a few weeks will be superseded by 16.04's release.
On 2/19/16 12:45 , Z K wrote:
Hello Yaroslav,
Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed. Ive update the wiki page:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out.
-Zeke
On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
Gotcha, thanks!
On February 18, 2016 3:27:21 PM EST, Z K zkaufman@nmr.mgh.harvard.edu wrote:
I would be infinitely grateful if freesurfer could build natively on
Debian
stable! ;) Thanks for trying. In my case I am trying the build
under jessie
chroot (using schroot helper), so I could quickly setup/enter such
environment
while maintaining user/directory. I will do the same now for 14.04.
If you
would like more -- let me know I could give a bit more detailed instructions.
I have a debian jessie system just setup, but I have a high priority project due Monday, so I would be able to begin determining the exact build procedure on Debian jessie until beginning of next week. It is something I have been meaning to do so I plan on getting to it. If you dont hear from me by Tuesday/Wedensday feel free to shoot me an email for an update. Thanks.
-Zeke
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
On Fri, 19 Feb 2016, Z K wrote:
Hello Yaroslav,
Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed.
I had tcsh but not libtool-bin installed in that chroot... heh
Ive update the wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out.
sweet! thanks. I will give it a shot!
in my case I have got stuck still on 14.04 trying to build with GUI but ./configure failed to find xawplus rightfully so since even centos6-x86_64-packages provides only a static build of it while configure sensing for a dynamic library. (and debian/ubuntus do not provide this antiquity)
I just wondered how do you guys build against it then? ;)
On Fri, 19 Feb 2016, Yaroslav Halchenko wrote:
On Fri, 19 Feb 2016, Z K wrote:
I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out.
sweet! thanks. I will give it a shot!
in my case I have got stuck still on 14.04 trying to build with GUI but ./configure failed to find xawplus rightfully so since even centos6-x86_64-packages provides only a static build of it while configure sensing for a dynamic library. (and debian/ubuntus do not provide this antiquity)
I just wondered how do you guys build against it then? ;)
Hi Z K,
and I guess it didn't even matter somehow while building under jessie with GUI enabled (after your patch for lapack multiple definitions and my patch for DESTDIR). FWIW -- success, I have managed to build the beast and it seems even to work ;) hip hip hoorray!
next question: I see some test files spread out through the code-base. Is there some centralized/uniform way to run them???
Thanks in advance!
freesurfer@nmr.mgh.harvard.edu
-
Rudolph Pienaar -
Yaroslav Halchenko -
Z K