[MINC-users] Official Installation Instructions

[Vladimir S. Fonov]

Hello,

On 12-07-02 10:04 PM, Mishkin Derakhshan wrote:
> I don't want to turn this into a "please help me with my installation"
> thread, but here is the summary of my results. The good news is that 2
> out of the 3 methods I tried worked! In true minc fashion there is
> more than one way to get 'er done.
> That being said, I still think it is frustrating for an end user to
> figure out which of the three they should have used.
>
> 1. http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit
> using the 32-bit version of the toolkit, and the testsuite and the models.
> I did have to run sudo apt-get install -f afterwards to install the
> missing library (libjpeg or something like that), but all appears to
> have installed okay. mincbeast in the pipeline does fail, but
> register, Display, mincstats etc. seem to work fine.
> ERROR! Allocation failure. Probably out of memory in
> /home/vfonov/src/minc-toolkit/BEaST/alloc.c:186.
> Died at /opt/minc/pipeline/pipeline_mritotal.pl line 182.
> (Odd that /home/vfonov is hardcoded into the error msg?)

yes, this error is noted in the 
http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit

Caveat Emptor: Unfortunately, currently mincbeast is unable to run in 
32bit mode properly, so standard_pipelene.pl will fail (and the 
test-suite will also fail)


So, if you would like to eliminate it, you can try following:

solution a: optimizing mincbeast ( https://github.com/BIC-MNI/BEaST )
so it fits in a 2Gb memory limit of 32 bit OS

solution b: install 64 bit version of Ubuntu.


> 3. https://github.com/BIC-MNI/minc-toolkit
> I tried compiling from source from git-hub using cmake. I ran into
> these problems:
> (i) ssh-keys for github.
> cd ../Register
>    git submodule init
>    git submodule update --recursive
> fatal: The remote end hung up unexpectedly
> Solution: https://help.github.com/articles/generating-ssh-keys

- looks like a broken url in the git submodule, so something didn't 
check out from git-hub prooperly, hence you can't compile some of the 
parts (and the rest of error messages).

-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com