[MINC-users] new minc-toolkit binary package

[Vladimir S. FONOV]

Hello Everybody,

thank you for testing, I've updated my test package and models
package, here are the new versions for Debian/Ubuntu:
http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.deb
http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.deb

And for Mac OS X:
http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.dmg
http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.dmg


On Sat, Apr 21, 2012 at 1:19 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hi Vlad,
>
> Very nice work building these packages!
>
> I installed and ran the test on OSX Lion, and it looks like the
> classification tag files are missing/misnamed/mislocated in your test
> pipeline:
>
> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_bg.tag
> does not exist
> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_prob_90_nobg.tag
> does not exist
>
> However these two:
>
> /opt/minc/share/classify/ntags_1000_bg.tag
> /opt/minc/share/classify/ntags_1000_prob_90_nobg.tag
>
> do exist
>
> -- A
>
> On Sat, Apr 21, 2012 at 1:02 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com> wrote:
>> Hello Everybody,
>>
>> it turns out that test suit /opt/minc/run_tests.sh is incompatible
>> with dash (Ubuntu replacement for bash), so to run it on ubuntu you
>> might have to execute it using bash explicitly i.e:
>>
>> bash /opt/minc/run_tests.sh <prefix>
>>
>> On Fri, Apr 20, 2012 at 7:49 PM, Vladimir S. FONOV
>> <vladimir.fonov at gmail.com> wrote:
>>> Hello Everybody,
>>>
>>> I've created a binary destribution of most of commonly used minc tools
>>> in a single package:
>>>
>>> for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke
>>> also succesfully installed it on Ubuntu 10.10)
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb
>>>
>>> for Debian 6:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb
>>>
>>> for MacOS X 10.7:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg
>>>
>>> It includes most of the standard minc tools, Display, Register and a
>>> basic image processing pipeline based on the one developed for NIHPD
>>> project ( standard_pipeline.pl) Everything is currently installed in
>>> /opt/minc , to avoid conflict with standard /usr/local/bic location.
>>> To use , source evironment in /opt/minc/minc-toolkit-config.sh for
>>> bash or /opt/minc/minc-toolkit-config.csh for tcsh
>>>
>>> Unfortunately, Display and Register  show everything in pink on MacOS X - maybe
>>> somebody with mac knowledge could take a look at it.
>>>
>>> The package is based on minc-toolkit superbuild package hosted on github:
>>>
>>> https://github.com/BIC-MNI/minc-toolkit
>>>
>>> If you feel like build it, read  README.txt at the bottom of github page
>>>
>>>
>>> Also, available collection of anatomical templates ( ICBM 152
>>> Nonlinear atlases version 2009 ):
>>>
>>> For Debian/Ubuntu:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb
>>>
>>> For MacOS X:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg
>>>
>>> anatomical templates will be installed in
>>> /opt/minc/share/icbm152_model_09a and
>>> /opt/minc/share/icbm152_model_09c
>>>
>>> I have also made a package for testing installation, right now it is
>>> running a standard pipeline on two (supplied ) ICBM subjects:
>>>
>>> For Debian/Ubuntu:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb
>>>
>>> For MacOS X:
>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg
>>>
>>> Test data is installed in /opt/minc/share/testsuit/ , to run the test
>>> execute /opt/minc/run_tests.sh <prefix> , it will take around
>>> 30minutes on modern computer , the output will be in
>>> <prefix>/00200  and <prefix>/00201 and the log file will be saved in
>>> <prefix>/minc-toolkit-test-<date>.log
>>>
>>> It would be great if somebody with a Mac could install the package and
>>> execute the test suite , to make sure it works as expected (I didn't
>>> have a chance).
>>
>>
>>
>> --
>> Best regards,
>>
>>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com