[MINC-users] new minc-toolkit binary package

[Alex Zijdenbos]

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
>