[MINC-development] Debian package for ubuntu 12.04
Vladimir S. FONOV
vladimir.fonov at gmail.com
Fri Apr 13 09:07:58 EDT 2012
Hello Everybody,
it turns out that N3 is not working properly in the package mentioned
below - I am still investigating.
On 4/11/2012 6:11 PM, Nicolas Rannou wrote:
> Cool I'll try it tomorrow as soon as I arrive in my office!
>
> Thanks
> Nicolas
>
> On Wed, Apr 11, 2012 at 6:03 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
>
> Hello,
>
> ok, I figured out how to generate these files, I included the changes in
>
> http://www.bic.mni.mcgill.ca/~__vfonov/software/minc-toolkit-__0.3.2-20120411-Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7Evfonov/software/minc-toolkit-0.3.2-20120411-Linux-x86_64.deb>
>
>
> On 12-04-11 03:35 PM, Nicolas Rannou wrote:
>
> *in the new debian pacakge:*
> perl->MNI: ok
>
> -> auto : *missing*
> some files ok
>
> *make install from mni-perl:*
> perl->MNI: ok
> ->auto:*ok*
>
> some files ok
>
> On Wed, Apr 11, 2012 at 3:34 PM, Nicolas Rannou
> <nicolas.lists at gmail.com <mailto:nicolas.lists at gmail.com>
> <mailto:nicolas.lists at gmail.__com
> <mailto:nicolas.lists at gmail.com>>> wrote:
>
> Great!
>
> I gave it a shot and it looks like in the Perl directory, the
> "*auto*" directory is missing (not sure what it is, but is used by
> FreeSurfer as well...):
>
> *in the new debian pacakge:*
> perl->MNI-> some files OK
> some files ok
>
> *make install from mni-perl:*
> perl->auto->*missing*
> ->MNI-> some file OK
> some files ok
>
> Thanks,
>
>
> On Wed, Apr 11, 2012 at 1:18 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>
> <mailto:vladimir.fonov at gmail.__com
> <mailto:vladimir.fonov at gmail.com>>> wrote:
>
> Hello,
>
> I made a simple command to install files in
> /opt/minc/perl (also
> added PERL5LIB variable in
> /opt/minc/minc-toolkit-config.____sh )
>
> So, try it on
> http://www.bic.mni.mcgill.ca/~____vfonov/software/minc-__toolkit-__0.3.2-20120411-__Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7E__vfonov/software/minc-toolkit-__0.3.2-20120411-Linux-x86_64.__deb>
> <http://www.bic.mni.mcgill.ca/__%7Evfonov/software/minc-__toolkit-0.3.2-20120411-Linux-__x86_64.deb
> <http://www.bic.mni.mcgill.ca/%7Evfonov/software/minc-toolkit-0.3.2-20120411-Linux-x86_64.deb>>
>
>
>
> On 12-04-11 12:42 PM, Nicolas Rannou wrote:
>
> That would be great! but I'm not sure on how much
> work it
> involves.
>
> I'm currently testing FreeSurfer against minc2 debian
> (provided by you)
> + mni-perlib from github
>
> I'll keep you posted!
>
> Nicolas
>
> On Wed, Apr 11, 2012 at 12:31 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>
> <mailto:vladimir.fonov at gmail.__com
> <mailto:vladimir.fonov at gmail.com>>
> <mailto:vladimir.fonov at gmail. <mailto:vladimir.fonov at gmail.>____com
>
> <mailto:vladimir.fonov at gmail.__com
> <mailto:vladimir.fonov at gmail.com>>>> wrote:
>
> Hello,
>
> I can insert it into my package, but I will have to
> figure out how
> to deal with it using CMake
>
> On 12-04-11 12:22 PM, Nicolas Rannou wrote:
>
> Yes that's what I meant, sorry for the
> confusion!
>
> So I guess my best bet is to build it
> manually and
> install it where
> FreeSurfer is expecting it!
> And maybe work a Debian packaging to make it
> easy
> for people to use.
>
> Thanks,
> Nicolas
>
> On Wed, Apr 11, 2012 at 11:54 AM, Vladimir
> S. FONOV
> <v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info
> <mailto:v.s.fonov at ilmarin.info>__>__>__>> wrote:
>
> Hello Nicolas,
>
> I don't quite understand what Perl
> support means
> in this
> context. Do you
> mean mni-perllib package (
> https://github.com/______andrewjanke/mni-perllib
> <https://github.com/____andrewjanke/mni-perllib>
> <https://github.com/____andrewjanke/mni-perllib
> <https://github.com/__andrewjanke/mni-perllib>>
>
>
> <https://github.com/____andrewjanke/mni-perllib
> <https://github.com/__andrewjanke/mni-perllib>
> <https://github.com/__andrewjanke/mni-perllib
> <https://github.com/andrewjanke/mni-perllib>>> ) ?
>
> On 12-04-11 11:48 AM, Nicolas Rannou wrote:
> > Hi Vladimir,
> >
> > It looks like MINC is not built with Perl support in those
> packages... :(
> >
> > Is it correct and if so do you plan to integrate it at some
> point?
> > Is there any good way I can do it or help?
> >
> > It is unfortunately requiered by freesurfer...!
> >
> > Thanks and keep up the great work!
> > Nicolas
> >
> > On Mon, Apr 9, 2012 at 2:44 PM, Vladimir S. FONOV
> > <v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info
> <mailto:v.s.fonov at ilmarin.info>__>__>__>
>
>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>__>
> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info>
> <mailto:v.s.fonov at ilmarin.info
> <mailto:v.s.fonov at ilmarin.info>__>__>__>>> wrote:
> >
> > Hello,
> >
> >
> > we have moved minc development to
> > https://github.com/________organizations/BIC-MNI
> <https://github.com/______organizations/BIC-MNI>
> <https://github.com/______organizations/BIC-MNI
> <https://github.com/____organizations/BIC-MNI>>
>
> <https://github.com/______organizations/BIC-MNI
> <https://github.com/____organizations/BIC-MNI>
> <https://github.com/____organizations/BIC-MNI
> <https://github.com/__organizations/BIC-MNI>>>
>
> > <https://github.com/______organizations/BIC-MNI
> <https://github.com/____organizations/BIC-MNI>
> <https://github.com/____organizations/BIC-MNI
> <https://github.com/__organizations/BIC-MNI>>
> <https://github.com/____organizations/BIC-MNI
> <https://github.com/__organizations/BIC-MNI>
> <https://github.com/__organizations/BIC-MNI
> <https://github.com/organizations/BIC-MNI>>>>
> >
> > I have been working on making a unified minc package,
> but it
> still
> > work in progress.
> >
> > You can try
> >
> http://www.bic.mni.mcgill.ca/~________vfonov/software/minc-______toolkit-__0.3.0-20120408-______Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7E______vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb>
> <http://www.bic.mni.mcgill.ca/__%7E____vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7E____vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>>
> <http://www.bic.mni.mcgill.ca/____%7E__vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>
> <http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7E__vfonov/software/minc-toolkit-__0.3.0-20120408-Linux-x86_64.__deb>>>
> <http://www.bic.mni.mcgill.ca/______%7E__vfonov/software/minc-______toolkit-__0.3.0-20120408-______Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/____%7E__vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb>
> <http://www.bic.mni.mcgill.ca/____%7E__vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>>
> <http://www.bic.mni.mcgill.ca/____%7E__vfonov/software/minc-____toolkit-__0.3.0-20120408-____Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>
> <http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb
> <http://www.bic.mni.mcgill.ca/%7E__vfonov/software/minc-toolkit-__0.3.0-20120408-Linux-x86_64.__deb>>>>
>
> >
> <http://www.bic.mni.mcgill.ca/______%7Evfonov/software/minc-______toolkit-0.3.0-20120408-__Linux-____x86_64.deb
> <http://www.bic.mni.mcgill.ca/____%7Evfonov/software/minc-____toolkit-0.3.0-20120408-Linux-____x86_64.deb>
> <http://www.bic.mni.mcgill.ca/____%7Evfonov/software/minc-____toolkit-0.3.0-20120408-Linux-____x86_64.deb
> <http://www.bic.mni.mcgill.ca/__%7Evfonov/software/minc-__toolkit-0.3.0-20120408-Linux-__x86_64.deb>>
>
>
> <http://www.bic.mni.mcgill.ca/____%7Evfonov/software/minc-____toolkit-0.3.0-20120408-Linux-____x86_64.deb
> <http://www.bic.mni.mcgill.ca/__%7Evfonov/software/minc-__toolkit-0.3.0-20120408-Linux-__x86_64.deb>
> <http://www.bic.mni.mcgill.ca/__%7Evfonov/software/minc-__toolkit-0.3.0-20120408-Linux-__x86_64.deb
> <http://www.bic.mni.mcgill.ca/%7Evfonov/software/minc-toolkit-0.3.0-20120408-Linux-x86_64.deb>>>>
> > - compiled on Ubuntu 11.10 but with most dependencies
> built-in. All
> > the tools will be installed in /opt/minc (this is
> temporary
> place) ,
> > source /opt/minc/minc-toolkit-config.________sh to
>
> configure
>
> environment.
> >
> >
> >
> > On 4/9/2012 1:15 PM, Nicolas Rannou wrote:
> >
> > Hi all,
> >
> > Do you plan to provide Debian packages for 12.04
> before
> the next
> > release
> > of Ubuntu 12.04? (April 26th)
> >
> > We are using FreeSurfer, which requires libminc2
> and minc
> tools
> > such as N3.
> >
> > libminc2 is already available but for instance,
> mincbundles
> > appears to
> > be outdated.
> > freesurfer relies on nu_correct for instance.
> >
> > root at bilbao:~# apt-get install mincbundle
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > Some packages could not be installed. This may
> mean that
> you have
> > requested an impossible situation or if you are
> using the
> unstable
> > distribution that some required packages have not yet
> been created
> > or been moved out of Incoming.
> > The following information may help to resolve the
> situation:
> >
> > The following packages have unmet dependencies:
> > mincbundle : Depends: glutg3-dev but it is not
> installable
> > Depends: libsoqt3-dev but it is not
> installable
> > Depends: mincsample but it is not
> installable
> > Depends: mni-models-colin27-lin but it
> is not
> > installable
> > Depends: mni-models-icbm152-lin but it
> is not
> > installable
> > E: Unable to correct problems, you have held broken
> packages.
--
Best regards,
Vladimir.FONOV <at> gmail <dot> com
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