From jp at biospective.com  Thu Jan 11 12:39:32 2018
From: jp at biospective.com (Jean-Philippe Coutu)
Date: Thu, 11 Jan 2018 12:39:32 -0500
Subject: [MINC-users] Using pyminc on a Windows machine
Message-ID: <CANHs=MfuRgW_Rc21OhZTQtdqR36L0FWJRc3=_LcWP0DvH8B3Pw@mail.gmail.com>

Dear MINC users,

I was curious to know if anyone is using pyminc on Windows, or whether this
is possible.

My understanding is that you would need to compile libminc on Windows,
which pyminc is dependent on.

Has anyone compiled or tried to compile the minc-toolkit, or, more
specifically libminc, on Windows recently? How would one go about it?

Thanks,
JP

From vladimir.fonov at gmail.com  Thu Jan 11 14:07:13 2018
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Jan 2018 14:07:13 -0500
Subject: [MINC-users] Using pyminc on a Windows machine
In-Reply-To: <CANHs=MfuRgW_Rc21OhZTQtdqR36L0FWJRc3=_LcWP0DvH8B3Pw@mail.gmail.com>
References: <CANHs=MfuRgW_Rc21OhZTQtdqR36L0FWJRc3=_LcWP0DvH8B3Pw@mail.gmail.com>
Message-ID: <004ce41c-43ee-474a-d6cf-3862c029ab19@gmail.com>

Hello,


libminc is compiled for windows inside ITK 4.XX , but without minc1 
support (which you wouldn't need for pyminc anyway).


So, if you compile ITK 4.13 for windows, you will get libminc inside.

On 2018-01-11 12:39 PM, Jean-Philippe Coutu wrote:
> Dear MINC users,
> 
> I was curious to know if anyone is using pyminc on Windows, or whether this
> is possible.
> 
> My understanding is that you would need to compile libminc on Windows,
> which pyminc is dependent on.
> 
> Has anyone compiled or tried to compile the minc-toolkit, or, more
> specifically libminc, on Windows recently? How would one go about it?
> 
> Thanks,
> JP
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From gabriel.devenyi at mcgill.ca  Mon Jan 22 21:27:55 2018
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Mon, 22 Jan 2018 21:27:55 -0500
Subject: [MINC-users] [RFC] [WIP] minc-diff-labels,
	diff and patch tools for minc label files
Message-ID: <CAFQOoOrPBKBxbjNOgoK8Yr960eW+yqKjDu644QgHUhqicAWFeA@mail.gmail.com>

Hi minc-users,

Inspired by a discussion I had with Dr. Mallar Chakravary and Dr. Jason
Lerch about tracking changes of label files, I recently attempted to
produce a data format and tools to compute differences between label files,
and store and apply differences, akin to the diff and patch tools for
source code.

I've produced a proof of concept implementation of the diff and patch tools
at https://github.com/gdevenyi/minc-diff-labels

Its probably fragile in a number of places, particularly, renumbering of
labels. Right now it assumes the label files are dimensionally is the same.

My initial applications are
- tracking changes to manual label sets (maybe via special git diff hooks?
a la git-latexdiff, https://gitlab.com/git-latexdiff/git-latexdiff)
- Comparing segmentations from different tools/parameters for a
segmentation pipeline

I'd like to hear about your possible applications of something like this.
Comments and questions also welcome.

From vladimir.fonov at gmail.com  Wed Jan 24 14:23:55 2018
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 24 Jan 2018 14:23:55 -0500
Subject: [MINC-users] new version of minc-toolkit-v2 is release
Message-ID: <fd6d6c67-464c-3ed8-bedc-0b65c9271df7@gmail.com>

Hello Everybody,

I released a new version of the minc-toolkit-v2, version 1.9.16

It includes all the changes to libminc, minctools, Display, Register etc 
as of 20181117, also it is build based on NetCDF version 4.5.0, HDF5 
version 1.8.20 , ITK version 4.13.0


The links to download are here: http://bic-mni.github.io/

I also created several containers to simplify installation:

All Containers are based on Ubuntu 16.04 64bit and include R 3.4.3 + 
tidyverse + RMINC 1.5.1.0 , python 2.7 + pyminc + pyezminc + 
minc2_simple and also standard anatomical models and beast templates 
installed in /opt/minc

Docker minc-toolkit-v2 1.9.16: docker pull nistmni/minc-toolkit:1.9.16
Docker minc-toolkit-v1 1.0.09: docker pull nistmni/minc-toolkit:1.9.16
Singularity minc-toolkit-v2 1.9.16: singularity pull --name 
minc-toolkit-1.9.16.simg shub://vfonov/minc-toolkit-containers:1.9.16

Also I created containers without anatomical templates and visual tools 
(mostly to save space):

Docker minc-toolkit-v2 1.9.16: "docker pull nistmni/minc-toolkit-min:1.9.16"
Singulatity minc-toolkit-v2 1.9.16: "singularity pull --name 
minc-toolkit-1.9.16-min.simg 
shub://vfonov/vfonov/minc-toolkit-containers:1.9.16-min"


It is fairly easy to make your own containers, the source code for 
making containers from above are here: 
https://github.com/vfonov/minc-toolkit-containers

Also, if you need to build minc-toolkit for another distribution , you 
can modify docker-based build system: 
https://github.com/BIC-MNI/build_packages


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From vladimir.fonov at gmail.com  Wed Jan 24 15:33:14 2018
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 24 Jan 2018 15:33:14 -0500
Subject: [MINC-users] new version of minc-toolkit-v2 is release
In-Reply-To: <fd6d6c67-464c-3ed8-bedc-0b65c9271df7@gmail.com>
References: <fd6d6c67-464c-3ed8-bedc-0b65c9271df7@gmail.com>
Message-ID: <CAMCwi7MnSU4=BMmR_NBEGNqmmfVphzByxGXHRYPk2y+SPEwp7g@mail.gmail.com>

Hello Again,

small correction, the download link for MacOS X version is
http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20180117-Darwin-x86_64.dmg
tomorrow it will get updated to the correct one :
http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20180117-Darwin-10.8-x86_64.dmg

On 24 January 2018 at 14:23, Vladimir S. FONOV <vladimir.fonov at gmail.com>
wrote:

> Hello Everybody,
>
> I released a new version of the minc-toolkit-v2, version 1.9.16
>
> It includes all the changes to libminc, minctools, Display, Register etc
> as of 20181117, also it is build based on NetCDF version 4.5.0, HDF5
> version 1.8.20 , ITK version 4.13.0
>
>
> The links to download are here: http://bic-mni.github.io/
>
> I also created several containers to simplify installation:
>
> All Containers are based on Ubuntu 16.04 64bit and include R 3.4.3 +
> tidyverse + RMINC 1.5.1.0 , python 2.7 + pyminc + pyezminc + minc2_simple
> and also standard anatomical models and beast templates installed in
> /opt/minc
>
> Docker minc-toolkit-v2 1.9.16: docker pull nistmni/minc-toolkit:1.9.16
> Docker minc-toolkit-v1 1.0.09: docker pull nistmni/minc-toolkit:1.9.16
> Singularity minc-toolkit-v2 1.9.16: singularity pull --name
> minc-toolkit-1.9.16.simg shub://vfonov/minc-toolkit-containers:1.9.16
>
> Also I created containers without anatomical templates and visual tools
> (mostly to save space):
>
> Docker minc-toolkit-v2 1.9.16: "docker pull nistmni/minc-toolkit-min:1.9.1
> 6"
> Singulatity minc-toolkit-v2 1.9.16: "singularity pull --name
> minc-toolkit-1.9.16-min.simg shub://vfonov/vfonov/minc-tool
> kit-containers:1.9.16-min"
>
>
> It is fairly easy to make your own containers, the source code for making
> containers from above are here: https://github.com/vfonov/minc
> -toolkit-containers
>
> Also, if you need to build minc-toolkit for another distribution , you can
> modify docker-based build system: https://github.com/BIC-MNI/bui
> ld_packages
>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>



-- 
Best regards,

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