From baghdadi at phenogenomics.ca  Wed Aug  3 12:00:34 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Wed, 3 Aug 2011 12:00:34 -0400
Subject: [MINC-users] minc git
Message-ID: <27029142.79501312387234003.JavaMail.root@mail2.phenogenomics.ca>

Hi everyone,

just wanted to remind everyone that minc is now part of github (thank you Andrew for all your efforts),  
https://github.com/andrewjanke/minc/

you can check recent commits and so on, 
please feel free to send in any bug reports or patches.

In my case, I will make an extra effort if your bug or patch is "minc2" related!

Leila

From mishkind at gmail.com  Thu Aug 25 13:34:03 2011
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Thu, 25 Aug 2011 13:34:03 -0400
Subject: [MINC-users] brain-view
In-Reply-To: <CAG0CB23qqYk60xtPa7Ld46yDt2shFuF0h+eA1s8GzU8ktxcpGw@mail.gmail.com>
References: <CA+bvZcD9+SD6b1ESm4nkounojsYsY8anWm2dnfd1zvej8Cc2ng@mail.gmail.com>
	<CAG0CB23qqYk60xtPa7Ld46yDt2shFuF0h+eA1s8GzU8ktxcpGw@mail.gmail.com>
Message-ID: <CAB-GmL1V745Ls36kLgqDset8WKKp=9unzaR6mH-aWf7SKmoC_w@mail.gmail.com>

Any updates on brain-view. I downloaded the source
(brain-view2.0.1.tar.gz) but I am a bit lost without a configure or
Makefile or README.

The referenced wiki page on launchpad does not seem to exist anymore either.
http://wiki.phenogenomics.ca:8080/display/MICePub/brain-view

I need to build it on a 64-bit ubuntu 11.04 system. Is there a list of
what dependencies are required (what version of Coin/QT etc.).

thanks,
mishkin




On Fri, Jul 8, 2011 at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Emily,
>
> I have talked to Jason Lerch (the Author) and yes brain-view is still
> maintained. I have been building an older release for a while that is
> broken with later QT releases. Suffice to say I will be have a crack
> at building you a new .deb version tonight.
>
> For reference, the latest version of brain-view can be found here (in
> source form).
>
> ? https://launchpad.net/brain-view
>
> Thanks
>
>
> a
>
> On Fri, Jul 8, 2011 at 10:24, Emily Segal <emily at bic.mni.mcgill.ca> wrote:
>> Hi minc-users,
>> Is brain-view no longer being supported? I would like to install brain-view
>> but there does not seem to be an up-to-date package available that works
>> with my OS. I am running Ubuntu 10.04.
>> Please let me know what I can do to get it up and running.
>> Thanks,
>> Emily
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From jason at phenogenomics.ca  Thu Aug 25 13:45:31 2011
From: jason at phenogenomics.ca (Jason Lerch)
Date: Thu, 25 Aug 2011 13:45:31 -0400
Subject: [MINC-users] brain-view
In-Reply-To: <CAB-GmL1V745Ls36kLgqDset8WKKp=9unzaR6mH-aWf7SKmoC_w@mail.gmail.com>
References: <CA+bvZcD9+SD6b1ESm4nkounojsYsY8anWm2dnfd1zvej8Cc2ng@mail.gmail.com>
Message-ID: <2E57E0CC-DAF8-4A9B-9A81-8E42E39D2800@phenogenomics.ca>

The link address has changed slightly - it's:

https://wiki.phenogenomics.ca/display/MICePub/brain-view

And I believe that Andrew has recently created a package for it ... Andrew?

Jason

On 2011-08-25, at 1:34 PM, Mishkin Derakhshan wrote:

> Any updates on brain-view. I downloaded the source
> (brain-view2.0.1.tar.gz) but I am a bit lost without a configure or
> Makefile or README.
> 
> The referenced wiki page on launchpad does not seem to exist anymore either.
> http://wiki.phenogenomics.ca:8080/display/MICePub/brain-view
> 
> I need to build it on a 64-bit ubuntu 11.04 system. Is there a list of
> what dependencies are required (what version of Coin/QT etc.).
> 
> thanks,
> mishkin
> 
> 
> 
> 
> On Fri, Jul 8, 2011 at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
>> Hi Emily,
>> 
>> I have talked to Jason Lerch (the Author) and yes brain-view is still
>> maintained. I have been building an older release for a while that is
>> broken with later QT releases. Suffice to say I will be have a crack
>> at building you a new .deb version tonight.
>> 
>> For reference, the latest version of brain-view can be found here (in
>> source form).
>> 
>>   https://launchpad.net/brain-view
>> 
>> Thanks
>> 
>> 
>> a
>> 
>> On Fri, Jul 8, 2011 at 10:24, Emily Segal <emily at bic.mni.mcgill.ca> wrote:
>>> Hi minc-users,
>>> Is brain-view no longer being supported? I would like to install brain-view
>>> but there does not seem to be an up-to-date package available that works
>>> with my OS. I am running Ubuntu 10.04.
>>> Please let me know what I can do to get it up and running.
>>> Thanks,
>>> Emily
>>> 
>> _______________________________________________
>> 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


From vladimir.fonov at gmail.com  Thu Aug 25 13:56:41 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 25 Aug 2011 13:56:41 -0400
Subject: [MINC-users] brain-view
In-Reply-To: <2E57E0CC-DAF8-4A9B-9A81-8E42E39D2800@phenogenomics.ca>
References: <CA+bvZcD9+SD6b1ESm4nkounojsYsY8anWm2dnfd1zvej8Cc2ng@mail.gmail.com>
	<2E57E0CC-DAF8-4A9B-9A81-8E42E39D2800@phenogenomics.ca>
Message-ID: <4E568CD9.4030303@gmail.com>

Hello,

last time when I was building brain-view2-0.1 (downloaded from 
https://launchpad.net/brain-view) I had to use "Quarter 1.0.0 Preview 
Release" to compile the program (from 
http://ftp.coin3d.org/coin/src/all/Quarter-1.0.0-preview.tar.gz )


On 11-08-25 01:45 PM, Jason Lerch wrote:
> The link address has changed slightly - it's:
>
> https://wiki.phenogenomics.ca/display/MICePub/brain-view
>
> And I believe that Andrew has recently created a package for it ... Andrew?
>
> Jason
>
> On 2011-08-25, at 1:34 PM, Mishkin Derakhshan wrote:
>
>> Any updates on brain-view. I downloaded the source
>> (brain-view2.0.1.tar.gz) but I am a bit lost without a configure or
>> Makefile or README.
>>
>> The referenced wiki page on launchpad does not seem to exist anymore either.
>> http://wiki.phenogenomics.ca:8080/display/MICePub/brain-view
>>
>> I need to build it on a 64-bit ubuntu 11.04 system. Is there a list of
>> what dependencies are required (what version of Coin/QT etc.).
>>
>> thanks,
>> mishkin
>>
>>
>>
>>
>> On Fri, Jul 8, 2011 at 12:25 AM, Andrew Janke<a.janke at gmail.com>  wrote:
>>> Hi Emily,
>>>
>>> I have talked to Jason Lerch (the Author) and yes brain-view is still
>>> maintained. I have been building an older release for a while that is
>>> broken with later QT releases. Suffice to say I will be have a crack
>>> at building you a new .deb version tonight.
>>>
>>> For reference, the latest version of brain-view can be found here (in
>>> source form).
>>>
>>>    https://launchpad.net/brain-view
>>>
>>> Thanks
>>>
>>>
>>> a
>>>
>>> On Fri, Jul 8, 2011 at 10:24, Emily Segal<emily at bic.mni.mcgill.ca>  wrote:
>>>> Hi minc-users,
>>>> Is brain-view no longer being supported? I would like to install brain-view
>>>> but there does not seem to be an up-to-date package available that works
>>>> with my OS. I am running Ubuntu 10.04.
>>>> Please let me know what I can do to get it up and running.
>>>> Thanks,
>>>> Emily
>>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> 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

From a.janke at gmail.com  Fri Aug 26 00:42:12 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 26 Aug 2011 14:42:12 +1000
Subject: [MINC-users] brain-view
In-Reply-To: <4E568CD9.4030303@gmail.com>
References: <CA+bvZcD9+SD6b1ESm4nkounojsYsY8anWm2dnfd1zvej8Cc2ng@mail.gmail.com>
	<2E57E0CC-DAF8-4A9B-9A81-8E42E39D2800@phenogenomics.ca>
	<4E568CD9.4030303@gmail.com>
Message-ID: <CAG0CB231tYRK4SB0wpLEQZfYQmYu0foUUZNHxdfwRp2uLutr8w@mail.gmail.com>

Hi all,

Correct on a bunch of things. Quarter is a pain, the tgz you download
seems to need patching and even then the examples or something make
the build fail. Still here is what I managed last time I tried this:

   http://packages.bic.mni.mcgill.ca/beta/

You will find a Ubuntu 10.10 package for amd64 and a binary
brain-view2 file that seems to work for me.

Let me know if this works OK, if so I'll just perform something dirty
and turn the single executable into a package.

ta


a

On 26 August 2011 03:56, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> Hello,
>
> last time when I was building brain-view2-0.1 (downloaded from
> https://launchpad.net/brain-view) I had to use "Quarter 1.0.0 Preview
> Release" to compile the program (from
> http://ftp.coin3d.org/coin/src/all/Quarter-1.0.0-preview.tar.gz )
>

From a.janke at gmail.com  Fri Aug 26 00:42:57 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 26 Aug 2011 14:42:57 +1000
Subject: [MINC-users] brain-view
In-Reply-To: <CAB-GmL1V745Ls36kLgqDset8WKKp=9unzaR6mH-aWf7SKmoC_w@mail.gmail.com>
References: <CA+bvZcD9+SD6b1ESm4nkounojsYsY8anWm2dnfd1zvej8Cc2ng@mail.gmail.com>
	<CAG0CB23qqYk60xtPa7Ld46yDt2shFuF0h+eA1s8GzU8ktxcpGw@mail.gmail.com>
	<CAB-GmL1V745Ls36kLgqDset8WKKp=9unzaR6mH-aWf7SKmoC_w@mail.gmail.com>
Message-ID: <CAG0CB22SzGw1a1K5ppa6cfo4GY2aYWLhhCuCt5m9f8kS8szNSg@mail.gmail.com>

On 26 August 2011 03:34, Mishkin Derakhshan <mishkind at gmail.com> wrote:
>
> I need to build it on a 64-bit ubuntu 11.04 system. Is there a list of
> what dependencies are required (what version of Coin/QT etc.).

Here is the line of magic that I use:


$ sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev
fftw-dev libgsl0-dev libgetopt-tabular-perl libmni-perllib-perl
libxext-dev glutg3-dev libsoqt3-dev libxmu-dev libxi-dev imagemagick
libtext-format-perl libpcre++0 libpcre3 libsimage-dev libpcre++-dev


a

From haitao.ge at hotmail.com  Sun Aug 28 09:41:25 2011
From: haitao.ge at hotmail.com (Haitao Ge)
Date: Sun, 28 Aug 2011 21:41:25 +0800
Subject: [MINC-users] CIVET
Message-ID: <SNT111-DS25B83AA801334196ABAF87F9150@phx.gbl>

Hi all,

I have learned that CIVET  is a a fully automated comprehensive pipeline for anatomical neuroimaging. How can i download and install it. Or how i apply for the permission.

Thanks a lot,

Haitao

From a.janke at gmail.com  Sun Aug 28 20:26:00 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 29 Aug 2011 10:26:00 +1000
Subject: [MINC-users] CIVET
In-Reply-To: <SNT111-DS25B83AA801334196ABAF87F9150@phx.gbl>
References: <SNT111-DS25B83AA801334196ABAF87F9150@phx.gbl>
Message-ID: <CAG0CB2394j-aewrsev-Gk_v+H6ThR-9u46XYXJOWdtZstGRkmQ@mail.gmail.com>

Hi Haitao

On 28 August 2011 23:41, Haitao Ge <haitao.ge at hotmail.com> wrote:
> I have learned that CIVET ?is a a fully automated comprehensive pipeline for anatomical neuroimaging. How can i download and install it. Or how i apply for the permission.

You will need to email Alan Evans for CIVET:

   http://www.bic.mni.mcgill.ca/~alan/

Thanks


a

From lrisa87 at uw.edu  Mon Aug 29 19:23:47 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Mon, 29 Aug 2011 16:23:47 -0700
Subject: [MINC-users] Compute overlap?
Message-ID: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>

Hello MINC experts,

Is there a MINC tool that will compute overlaps (dice coefficient, jaccard
coefficient, etc)?

Thank you.


Best,
Lisa

From a.janke at gmail.com  Mon Aug 29 19:39:03 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 30 Aug 2011 09:39:03 +1000
Subject: [MINC-users] Compute overlap?
In-Reply-To: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
References: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
Message-ID: <CAG0CB23VpsEvL_FfVOam+yOumzeM73YQ1PkFNwWyF+H8VBW8tQ@mail.gmail.com>

Hi Lisa,

On 30 August 2011 09:23, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Is there a MINC tool that will compute overlaps (dice coefficient, jaccard
> coefficient, etc)?

You could compute a dice coefficient using mincmath and mincstats
assuming both volumes are masks:

   $ mincmath -and in1.mnc in2.mnc and.mnc
   $ nvox1=`mincstats -count -quiet in1.mnc`
   $ nvox2=`mincstats -count -quiet in2.mnc`
   $ nvoxand=`mincstats -count -quiet and.mnc`

   $ dice=`echo "(2 * $nvoxand) / ($nvox1 + $nvox2)" | bc -l`

Note that I haven't checked the above! but it should put you on the right track!

Other options are to write you own by adding a function to minccmp.
There is also a rather unfriendly tool in conglomerate called voldiff
that computes all sorts of wonderful segmentation comparison things.
It expects input to be in the same form as the output of classify
IIRC.  Perhaps someone else who has battled voldiff before can give
some insight.


a

From asko at hst.aau.dk  Tue Aug 30 09:25:02 2011
From: asko at hst.aau.dk (Anne Sofie Korsager)
Date: Tue, 30 Aug 2011 13:25:02 +0000
Subject: [MINC-users] Rotations in minctracc
Message-ID: <DB9895A2989BB5468A846E10FE811B970669E4BA@AD-EXCHMBX2-1.aau.dk>

Hi,



How is it possible in Minctracc to define a non-orthogonal rotation (not a rotation around the image axes using w_rotations but a rotation around e.g. a vector)?



- Anne Sofie

From a.janke at gmail.com  Tue Aug 30 09:39:31 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 30 Aug 2011 23:39:31 +1000
Subject: [MINC-users] Rotations in minctracc
In-Reply-To: <DB9895A2989BB5468A846E10FE811B970669E4BA@AD-EXCHMBX2-1.aau.dk>
References: <DB9895A2989BB5468A846E10FE811B970669E4BA@AD-EXCHMBX2-1.aau.dk>
Message-ID: <CAG0CB22NADe=CyEJB=UxF9YsbO8T8PBqnVp2WVo7gsBWrsSkxA@mail.gmail.com>

Hi Anne,

> How is it possible in Minctracc to define a non-orthogonal rotation (not a rotation around the image axes using w_rotations but a rotation around e.g. a vector)?

Short version is I dont think it is possible.

So you have two choices.

1. create an xfm using param to xfm to resample your data such that
your vector is aligned with an axis. Use minctracc and then do a few
transformation concatenations (using xfmconcat) to get your resulting
xfm.   You can then apply this resulting xfm to your original
non-resampled data using mincresample.

2. There is code in mintracc to handle rotations using quaternions,
you might be able to modify the code such that you can assign weights
to the elements of the quaternion and thus set your initial axis of
rotation that way.

My guess is that #1 will be a whole lot easier.


a

From zijdenbos at gmail.com  Tue Aug 30 12:31:56 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 30 Aug 2011 12:31:56 -0400
Subject: [MINC-users] Compute overlap?
In-Reply-To: <CAG0CB23VpsEvL_FfVOam+yOumzeM73YQ1PkFNwWyF+H8VBW8tQ@mail.gmail.com>
References: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
	<CAG0CB23VpsEvL_FfVOam+yOumzeM73YQ1PkFNwWyF+H8VBW8tQ@mail.gmail.com>
Message-ID: <CABEEk16+qnfR5SXhL-vhMWtLoM4g9ssB_00TLsZ_KUqRp0nccw@mail.gmail.com>

On Mon, Aug 29, 2011 at 7:39 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Lisa,
>
> On 30 August 2011 09:23, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>> Is there a MINC tool that will compute overlaps (dice coefficient, jaccard
>> coefficient, etc)?
>
> You could compute a dice coefficient using mincmath and mincstats
> assuming both volumes are masks:
>
> ? $ mincmath -and in1.mnc in2.mnc and.mnc
> ? $ nvox1=`mincstats -count -quiet in1.mnc`
> ? $ nvox2=`mincstats -count -quiet in2.mnc`
> ? $ nvoxand=`mincstats -count -quiet and.mnc`
>
> ? $ dice=`echo "(2 * $nvoxand) / ($nvox1 + $nvox2)" | bc -l`
>
> Note that I haven't checked the above! but it should put you on the right track!

Looks good to me - I have a bit of perl code that does essentially the
same thing:

sub Dice {
    my ($vol1, $vol2) = @_;

    my $sum = &TmpFile('masksum');

    &Run(['mincmath', '-clobber', '-add', $vol1, $vol2, $sum]) && die;

    my @stats;
    &Run(['mincstats', '-quiet', '-count', '-binvalue', '1,2', $sum],
\@stats) && die;
    chomp @stats;

    return (2.0 * $stats[1]) / (2.0 * $stats[1] + $stats[0]);
}

> Other options are to write you own by adding a function to minccmp.
> There is also a rather unfriendly tool in conglomerate called voldiff
> that computes all sorts of wonderful segmentation comparison things.
> It expects input to be in the same form as the output of classify
> IIRC. ?Perhaps someone else who has battled voldiff before can give
> some insight.

Voldiff was written by Vasco Kollokian in days long gone by; it
generates a variety of metrics derived from a confusion matrix that
may be non-dichotomous (multi-class segmentations). It indeed expects
"standard" output from classify, with labels 1,2, and 3 for CSF, GM,
and WM, respectively, but I think it should work for the more general
case as well. It's output is rather verbose so can be a bit tricky to
parse.

In some ideal world I think similar functionality would end up in
minccmp; that just requires somebody to spend enough time to add it :)

-- A

From a.janke at gmail.com  Wed Aug 31 09:44:32 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 31 Aug 2011 23:44:32 +1000
Subject: [MINC-users] Compute overlap?
In-Reply-To: <CABEEk16+qnfR5SXhL-vhMWtLoM4g9ssB_00TLsZ_KUqRp0nccw@mail.gmail.com>
References: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
	<CAG0CB23VpsEvL_FfVOam+yOumzeM73YQ1PkFNwWyF+H8VBW8tQ@mail.gmail.com>
	<CABEEk16+qnfR5SXhL-vhMWtLoM4g9ssB_00TLsZ_KUqRp0nccw@mail.gmail.com>
Message-ID: <CAG0CB20B4HiJGZESdu9z_OgZYV3nAARDPhLn63wUaYNkkAXw=Q@mail.gmail.com>

Hi Alex,

On 31 August 2011 02:31, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> ? ?return (2.0 * $stats[1]) / (2.0 * $stats[1] + $stats[0]);

You sure of that 2.0 * in the denominator?

Wikipedia says something different:

   http://en.wikipedia.org/wiki/Dice%27s_coefficient

Although I am sure there are more things to compare with than just
Dice's coefficient.


a

From zijdenbos at gmail.com  Wed Aug 31 10:09:52 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 31 Aug 2011 10:09:52 -0400
Subject: [MINC-users] Compute overlap?
In-Reply-To: <CAG0CB20B4HiJGZESdu9z_OgZYV3nAARDPhLn63wUaYNkkAXw=Q@mail.gmail.com>
References: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
	<CAG0CB23VpsEvL_FfVOam+yOumzeM73YQ1PkFNwWyF+H8VBW8tQ@mail.gmail.com>
	<CABEEk16+qnfR5SXhL-vhMWtLoM4g9ssB_00TLsZ_KUqRp0nccw@mail.gmail.com>
	<CAG0CB20B4HiJGZESdu9z_OgZYV3nAARDPhLn63wUaYNkkAXw=Q@mail.gmail.com>
Message-ID: <CABEEk17qJ9N3Ew8JGBNS4WN7TqSz1d-XpooxxB3YTBbtFQtJ4g@mail.gmail.com>

On Wed, Aug 31, 2011 at 9:44 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Alex,
>
> On 31 August 2011 02:31, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>> ? ?return (2.0 * $stats[1]) / (2.0 * $stats[1] + $stats[0]);
>
> You sure of that 2.0 * in the denominator?

Yup :)

> Wikipedia says something different:
>
> ? http://en.wikipedia.org/wiki/Dice%27s_coefficient

Actually, it does not; the difference is that I use -add in the
mincmath call, so $stats[1] becomes n_intersection, and $stats[0] is
the sum of the relative complements. In other words, if the regions
are A and B, you calculate the denominator as

 n(A) + n(B)

which is equal to

 2 * n(A ^ B) + n(A\B) + n(B\A)

which is what I calculate (couldn't find the correct math symbols but
you get the picture). Same difference though.

> Although I am sure there are more things to compare with than just
> Dice's coefficient.

That too - I'm always fascinated how many ways there are to turn the 4
values of a 2x2 confusion matrix into a number :) voldiff calculates
some but there are many more.

-- A

From a.janke at gmail.com  Wed Aug 31 10:17:32 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 1 Sep 2011 00:17:32 +1000
Subject: [MINC-users] Compute overlap?
In-Reply-To: <CABEEk17qJ9N3Ew8JGBNS4WN7TqSz1d-XpooxxB3YTBbtFQtJ4g@mail.gmail.com>
References: <CAKpVfoMNiuak8GNyJ=-6AkdwpTq0n2aFei=BwgzQntafyhGwoQ@mail.gmail.com>
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>> ? http://en.wikipedia.org/wiki/Dice%27s_coefficient
>
> Actually, it does not; the difference is that I use -add in the
> mincmath call, so $stats[1] becomes n_intersection, and $stats[0] is
> the sum of the relative complements. In other words, if the regions
> are A and B, you calculate the denominator as
>
> ?n(A) + n(B)
>
> which is equal to
>
> ?2 * n(A ^ B) + n(A\B) + n(B\A)

Ah, now I am with you....

>> Although I am sure there are more things to compare with than just
>> Dice's coefficient.
>
> That too - I'm always fascinated how many ways there are to turn the 4
> values of a 2x2 confusion matrix into a number :) voldiff calculates
> some but there are many more.

Aye, I got half way through re-implementing the core of voldiff in
minccmp for integer input volumes a while back but gave up with all
the seemingly multiple contradictory definitions of how things should
be done with a n x n confusion matrix across a variable number of
files!  (you'll see a commented out -kappa option in there).

All this talk of binary comparisons has got me all energised to finish
it off again...


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