[MINC-users] new minc-toolkit binary package

Tue Apr 24 21:06:03 EDT 2012

Hello Everybody,

we (me and Louis) have created an official page for minc-tollkit :
http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit
It contains links to latest versions of binary packages.

Also, I have included pre-compiled third-party binary packages of
ITK-SNAP with minc support and elastix also with minc support.

On Sun, Apr 22, 2012 at 12:04 AM, Vladimir S. FONOV
<vladimir.fonov at gmail.com> wrote:
> 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

-- 
Best regards,

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