Hello Yaroslav,
I believe there is already an option that can be set at configure time to build
dynamical;ly, though
I have not tried it. e.g., maybe it causes the libraries that
Freesurfer builds internally to be built as shared instead of static.
However, at least in out nightly builds, the fr
Dear FreeSurfer developers,
I would like to pick up on this elderly theme by wondering:
Would you be philosophically opposed against patches/pull requests
which introduce dynamic linking for freesurfer build?
Would anyone from the FreeSurfer team be interested to pursue such
an effort?
The id
On Sun, 21 Feb 2016, R Edgar wrote:
> On 21 February 2016 at 22:33, wrote:
> > Intolerable differences have not been found. They are always minor <%5 and
> > their source can come from several places. For example, different
> > compilers (or even different versions of the same compiler) can hav
On Sun, 21 Feb 2016, zkauf...@nmr.mgh.harvard.edu wrote:
> This topic gets brought up occasionally and their are valid arguments
> to both sides. One reason we have hesitated to use dynamic libs is the
> partly due to freesurfers long release cycle (all subjects that are
> part of a study need to
On 21 February 2016 at 22:33, wrote:
> Intolerable differences have not been found. They are always minor <%5 and
> their source can come from several places. For example, different
> compilers (or even different versions of the same compiler) can have
> different sorting behavior when presented
Yes this is a good idea. All subsequent 3rd party bundles will be
versioned as (or similar to) the way you describe below. Which is good
because a new one will be released soon. Thanks for the input.
-Zeke
> ATM
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/ce
Intolerable differences have not been found. They are always minor <%5 and
their source can come from several places. For example, different
compilers (or even different versions of the same compiler) can have
different sorting behavior when presented with objects that have
equivalent comparators.
This topic gets brought up occasionally and their are valid arguments to
both sides. One reason we have hesitated to use dynamic libs is the partly
due to freesurfers long release cycle (all subjects that are part of a
study need to be performed all on the same version). This long release
cycle som
ATM
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz
has no versioned counterpart. Could you please provide some versioning
e.g. by actually having
centos6-x86_64-packages-0.0.20151104.tar.gz (based on its modification
date, 0.0. to
On 20 February 2016 at 17:28, Bruce Fischl wrote:
> hmmm, the only thing that worries me about dynamic linking is that it
> will add variability to the outputs. Zeke has spent endless amounts of time
> tracking down e.g. mac vs. pc differences in math libs and such.
What sort of differences were
On Sat, 20 Feb 2016, Bruce Fischl wrote:
> hmmm, the only thing that worries me about dynamic linking is that it
> will add variability to the outputs. Zeke has spent endless amounts of time
> tracking down e.g. mac vs. pc differences in math libs and such. Won't
> dynamic linking just make th
hmmm, the only thing that worries me about dynamic linking is that it
will add variability to the outputs. Zeke has spent endless amounts of time
tracking down e.g. mac vs. pc differences in math libs and such. Won't
dynamic linking just make that a much more prevalent problem?
Bruce
On Sat,
Hi again,
While our "building from source" discussion is "hot" I wondered to ask
if there was an attempt or may be plans for to switch to using dynamic
linking (and collect functionality within a few internal
libraries) instead of static duplication of binary code across
binaries.
At some point M
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 getti
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 th
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
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 fe
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 quit
On Thu, 18 Feb 2016, Z K wrote:
> > is there a public clone of freesurfer on github?
> Sorry, their is no public freesurfer on github. But at the current
> moment (and forseeable future) the public repo is an exact mirro of the
> private repo.
> > --disable-GUI-build -- wouldn't it disable t
>
> is there a public clone of freesurfer on github?
Sorry, their is no public freesurfer on github. But at the current
moment (and forseeable future) the public repo is an exact mirro of the
private repo.
>
> --disable-GUI-build -- wouldn't it disable then building all so necessary GUI
> too
On Thu, 18 Feb 2016, Z K wrote:
> I beleive the .travis.yml does work but it is still under active
> development.
is there a public clone of freesurfer on github?
> The Ubuntu instructions in the linux developers page have been tested on a
> clean install and should work
> (https://surfer.nmr.m
Hello,
I beleive the .travis.yml does work but it is still under active
development.
The Ubuntu instructions in the linux developers page have been tested on
a clean install and should work
(https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page).
However I have not yet
Hi Z K et al,
What would be the recommended/tested debian/ubuntu release to approach the
build with some guarantee of success? Is the .travis.yml "exercised" (failed
to quickly find a sign of it on travis-ci.org)?
I have tried on debian jessie to build stable5_branch-5622-gf3d0bcd of
the git/ann
Hello Alle,
The naming of "configure.in" vs. "configure.ac" is not the issue. The
script is erroring out because file 'm4/autotroll.m4' does not exist. Do
you have that file (it should have been included in the checkout)?
I would recommend using our git repo which mirrors our CVS repo. Please
I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system.
(64 bit, using g++ 4.9 for compilation)
After
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
checkout -P dev
$ cd dev
$ cvs upda
Nick,
On Wednesday 11 January 2012 11:52:19 Nick Schmansky wrote:
> it appears the recon-all proceeded successfully all the way to nearly
> the end. it failed in some new code (you are working with our
> 'development' checkout, so new stuff often breaks the stream), so i'll
> have to pass that
malcolm,
hi, i'm able to replicate that warning on that data, and i'm
investigating. i would say its a false alarm, as that input data is
considered 'optimal' (mprage from our own scanners).
it appears the recon-all proceeded successfully all the way to nearly
the end. it failed in some new co
malcolm,
running 'make check' is one way to check the build. we run that nightly
on our three build platforms (linux 32b, 64b and mac leopard). a goal
of our linux centos build is to have it run on as many linux variants as
possible without people having to modify their local install, and to
tha
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which
seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l
407
I did have one fa
Nick,
While configure now works, I'm getting a build-time error.
It looks like:
histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers
Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new depe
Nick,
With the new configure.in, --disable-all-apps works as advertised.
Thanks!
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
> malcolm,
>
> can you try using the attached configure.in? you will need to
> run ./setup_configure, which will create a new configure script.
>
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
> Nick,
>
> Tcl/Tk is installed on the system under /usr/bin so I can't e
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my
path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl-
apps) be considered broken? Any other suggestions for a work-around? Would a
c
the other way to build w/o gui support is to exclude the tcl and vtk
paths in configure. in other works, only vtk and mni should be included
in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
> I'm attempting to build the development branch of the source code.
> To
I'm attempting to build the development branch of the source code.
To reduce dependencies, I'm trying to build without any of the GUI support
using the flags:
--disable-all-apps
--disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check conf
x86 was a typo. I mean POWER5
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/24 Pedro Paulo de Magalhães Oliveira Junior
> I have one AIX version
I have one AIX version. Is it x86?
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/24 Michael Scheel
> I have the opportunity to run my analysis w
Hi everybody,
I have the opportunity to run my analysis with freesurfer on a big
computer-cluster that is running on AIX.
However to install freesurfer there I need to build it from source. Is
the source code available?
I found some older entries in the archives and the issue seemed at
that
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