From storelli.loredana at hsr.it  Wed Feb  3 10:58:33 2016
From: storelli.loredana at hsr.it (Storelli Loredana)
Date: Wed, 3 Feb 2016 15:58:33 +0000
Subject: [MINC-users] help FLAIR simulation
Message-ID: <AM4PR02MB12667E6A5593BB61AD68632486D00@AM4PR02MB1266.eurprd02.prod.outlook.com>

Goodmorning,


I know that there aren't pre-simulated FLAIR sequences on the BrainWeb so I tried to produce it with the custom simulator, but also inserting FLAIR sequence parameters in an Inversion Recovery sequence I cannot obtain an image with the suppresion of the CSF as in the FLAIR.

Does anyone have some suggestions?

Thank you,


Loredana


Rispetta l'ambiente: non stampare questa mail se non ? necessario.
Respect the environment: if it's not necessary, don't print this mail.

From vladimir.fonov at gmail.com  Wed Feb 10 11:18:54 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 10 Feb 2016 11:18:54 -0500
Subject: [MINC-users] new release of minc-toolkit
Message-ID: <56BB62EE.1000708@gmail.com>

Hello Everybody,


I made a new release of minc-toolkit, standard branch - version 1.0.08 
and v2 branch - version 1.9.11.  It includes all the latest versions of 
minc tools (as of 2nd of February 2016). V2 branch includes ITK 4.9 
library and latest versions of ANTs and Elastix. V2 branch now also 
includes tools for patch-based segmentations ( see 
https://github.com/vfonov/patch_morphology ).

MacOSX version was updated to work properly on 10.11 ( El Capitan). 
Unfortunately I was not able to build v2 branch for older (10.7) 
version, so only the standard branch is available to folks who are stuck 
with old version of MacOS X.

All the binary packages are downloadable from 
http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit


Note that web page http://www.mcgill.ca/bic/software/minc/minctoolkit is 
out of date!
-- 
Best regards,

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

From gdevenyi at gmail.com  Thu Feb 11 09:53:08 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 09:53:08 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
Message-ID: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>

Hi minc-users,

I have successfully used xfmavg on lsq12 transforms numerous times with no
issues (and it runs great with pydpiper).

I recently tried to average some (very similar) lsq6 transforms and found
that the result is not at all what I expected, it is quite far off from the
inputs.

Do lsq6 transforms not satisfy the mathematical underpinnings of xfmavg or
is something else going on?

Thanks for your insight!

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From vladimir.fonov at gmail.com  Thu Feb 11 10:25:32 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Feb 2016 10:25:32 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
Message-ID: <CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>

What were your expectations and what did you get?

On Thu, Feb 11, 2016 at 9:53 AM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Hi minc-users,
>
> I have successfully used xfmavg on lsq12 transforms numerous times with no
> issues (and it runs great with pydpiper).
>
> I recently tried to average some (very similar) lsq6 transforms and found
> that the result is not at all what I expected, it is quite far off from the
> inputs.
>
> Do lsq6 transforms not satisfy the mathematical underpinnings of xfmavg or
> is something else going on?
>
> Thanks for your insight!
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> 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 zijdenbos at gmail.com  Thu Feb 11 10:33:00 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 11 Feb 2016 10:33:00 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
Message-ID: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>

Hi all,

I got some 3D DICOM SPECT data that dcm2mnc issues with - depending on what
version of dcm2mnc I use, I get somewhat different results; but in most
cases I end up with irregular z-spacing and/or a flipped z-axis. The most
recent version I tried was dcm2mnc version 2.01.03 from minc-toolkit
version 1.0.08.

If I run the same thing through dcm2nii followed by nii2mnc (ugh!), I
actually get a volume that looks like I expected. There appears to be
coordinate space information in the 3D DICOM that dcm2nii seems to be able
to interpret, but dcm2mnc does not.

Thoughts/pointers/updated versions of dcm2mnc?

Here is a sample DICOM set:
?
 s1_0013006_3006.dcm.gz
<https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web>
?

Thanks,

-- A

From robert.d.vincent at mcgill.ca  Thu Feb 11 10:47:22 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Thu, 11 Feb 2016 10:47:22 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
Message-ID: <CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>

Hi Alex,

We've encountered so little 3D DICOM over the years I'm not surprised it
isn't handled well.

Thanks for the dataset. I will look into it and let you know.

    -bert


On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <zijdenbos at gmail.com>
wrote:

> Hi all,
>
> I got some 3D DICOM SPECT data that dcm2mnc issues with - depending on what
> version of dcm2mnc I use, I get somewhat different results; but in most
> cases I end up with irregular z-spacing and/or a flipped z-axis. The most
> recent version I tried was dcm2mnc version 2.01.03 from minc-toolkit
> version 1.0.08.
>
> If I run the same thing through dcm2nii followed by nii2mnc (ugh!), I
> actually get a volume that looks like I expected. There appears to be
> coordinate space information in the 3D DICOM that dcm2nii seems to be able
> to interpret, but dcm2mnc does not.
>
> Thoughts/pointers/updated versions of dcm2mnc?
>
> Here is a sample DICOM set:
> ?
>  s1_0013006_3006.dcm.gz
> <
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> >
> ?
>
> Thanks,
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Thu Feb 11 10:55:05 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 10:55:05 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
Message-ID: <CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>

Sure, easiest to expose with xfm2param:

#One of 32 transforms
> xfm2param input1.xfm
after parameter extraction
-center         0.00000    0.00000    0.00000
-translation    0.70513    0.30790    0.66079
-rotation     -87.58608    4.54388    2.03792
-scale          1.00000    1.00000    1.00000
-shear         -0.00000   -0.00000    0.00000

#Transforms have rotations in range 83-92 -6-7 -2 4
> xfmavg *.xfm average.xfm
> xfm2param average.xfm
after parameter extraction
-center         0.00000    0.00000    0.00000
-translation    0.38288    0.50712    0.52295
-rotation      -0.04862    0.66666   -0.63100
-scale          1.00000    1.00000    1.00000
-shear         -0.00000   -0.00000    0.00000

#Rotations have been completely lost

I just realized this may be due to the values since they?re near -90, could
this be a problem?
?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 10:25 AM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> What were your expectations and what did you get?
>
> On Thu, Feb 11, 2016 at 9:53 AM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
> > Hi minc-users,
> >
> > I have successfully used xfmavg on lsq12 transforms numerous times with
> no
> > issues (and it runs great with pydpiper).
> >
> > I recently tried to average some (very similar) lsq6 transforms and found
> > that the result is not at all what I expected, it is quite far off from
> the
> > inputs.
> >
> > Do lsq6 transforms not satisfy the mathematical underpinnings of xfmavg
> or
> > is something else going on?
> >
> > Thanks for your insight!
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> > _______________________________________________
> > 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Thu Feb 11 10:59:05 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 10:59:05 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
Message-ID: <CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>

Just a follwup, the "newer" dicom creator is dcm2niix, may be able to find
some useful info here https://github.com/neurolabusc/dcm2niix

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Alex,
>
> We've encountered so little 3D DICOM over the years I'm not surprised it
> isn't handled well.
>
> Thanks for the dataset. I will look into it and let you know.
>
>     -bert
>
>
> On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi all,
> >
> > I got some 3D DICOM SPECT data that dcm2mnc issues with - depending on
> what
> > version of dcm2mnc I use, I get somewhat different results; but in most
> > cases I end up with irregular z-spacing and/or a flipped z-axis. The most
> > recent version I tried was dcm2mnc version 2.01.03 from minc-toolkit
> > version 1.0.08.
> >
> > If I run the same thing through dcm2nii followed by nii2mnc (ugh!), I
> > actually get a volume that looks like I expected. There appears to be
> > coordinate space information in the 3D DICOM that dcm2nii seems to be
> able
> > to interpret, but dcm2mnc does not.
> >
> > Thoughts/pointers/updated versions of dcm2mnc?
> >
> > Here is a sample DICOM set:
> > ?
> >  s1_0013006_3006.dcm.gz
> > <
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > >
> > ?
> >
> > Thanks,
> >
> > -- A
> > _______________________________________________
> > 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 hihemanth08 at gmail.com  Thu Feb 11 11:18:58 2016
From: hihemanth08 at gmail.com (Hemanth I (Hemambaradarahara   Rao))
Date: Thu, 11 Feb 2016 21:48:58 +0530
Subject: [MINC-users] MINC-users Digest, Vol 126, Issue 2
In-Reply-To: <mailman.7.1455123602.7511.minc-users@bic.mni.mcgill.ca>
References: <mailman.7.1455123602.7511.minc-users@bic.mni.mcgill.ca>
Message-ID: <CAH7=K=X=WZ6HaKBWi3dEjSBh=KntdM8JzCjxe6zcoiKeQaBc4Q@mail.gmail.com>

Hii minc -users,
I am using minc format brain images for wavelet based image fusion.
Can i use this tool kit for image segmentation if possible can anybody
explain how to use this toolkit for image segmentation.
I am using both ubuntu 14.04 and windows 8.1 so tool kits in ubuntu or
windows both i can use.if anyone know about image segmentation for minc
images using these tool kits please do respond it will be helpful for me.


Thank you

On Wed, Feb 10, 2016 at 10:30 PM, <minc-users-request at bic.mni.mcgill.ca>
wrote:

> Send MINC-users mailing list submissions to
>         minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
>         minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
>         minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
>
> Today's Topics:
>
>    1. new release of minc-toolkit (Vladimir S. FONOV)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Feb 2016 11:18:54 -0500
> From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] new release of minc-toolkit
> Message-ID: <56BB62EE.1000708 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Everybody,
>
>
> I made a new release of minc-toolkit, standard branch - version 1.0.08
> and v2 branch - version 1.9.11.  It includes all the latest versions of
> minc tools (as of 2nd of February 2016). V2 branch includes ITK 4.9
> library and latest versions of ANTs and Elastix. V2 branch now also
> includes tools for patch-based segmentations ( see
> https://github.com/vfonov/patch_morphology ).
>
> MacOSX version was updated to work properly on 10.11 ( El Capitan).
> Unfortunately I was not able to build v2 branch for older (10.7)
> version, so only the standard branch is available to folks who are stuck
> with old version of MacOS X.
>
> All the binary packages are downloadable from
> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit
>
>
> Note that web page http://www.mcgill.ca/bic/software/minc/minctoolkit is
> out of date!
> --
> Best regards,
>
>   Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>
>
> ------------------------------
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> End of MINC-users Digest, Vol 126, Issue 2
> ******************************************
>



-- 
Best Regards
Hemanth Indlamuri

From vladimir.fonov at gmail.com  Thu Feb 11 11:33:13 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Feb 2016 11:33:13 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
Message-ID: <56BCB7C9.1090502@gmail.com>

Maybe it would be easier if you would make all xfms available...


On 16-02-11 10:55 AM, Gabriel A. Devenyi wrote:
> Sure, easiest to expose with xfm2param:
>
> #One of 32 transforms
>> xfm2param input1.xfm
> after parameter extraction
> -center         0.00000    0.00000    0.00000
> -translation    0.70513    0.30790    0.66079
> -rotation     -87.58608    4.54388    2.03792
> -scale          1.00000    1.00000    1.00000
> -shear         -0.00000   -0.00000    0.00000
>
> #Transforms have rotations in range 83-92 -6-7 -2 4
>> xfmavg *.xfm average.xfm
>> xfm2param average.xfm
> after parameter extraction
> -center         0.00000    0.00000    0.00000
> -translation    0.38288    0.50712    0.52295
> -rotation      -0.04862    0.66666   -0.63100
> -scale          1.00000    1.00000    1.00000
> -shear         -0.00000   -0.00000    0.00000
>
> #Rotations have been completely lost
>
> I just realized this may be due to the values since they?re near -90, could
> this be a problem?
> ?
>


-- 
Best regards,

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

From gdevenyi at gmail.com  Thu Feb 11 11:40:43 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 11:40:43 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <56BCB7C9.1090502@gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
Message-ID: <CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>

https://www.dropbox.com/s/vk9zzile5ox7pu4/transforms.tar.bz2?dl=0

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 11:33 AM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> Maybe it would be easier if you would make all xfms available...
>
>
> On 16-02-11 10:55 AM, Gabriel A. Devenyi wrote:
>
>> Sure, easiest to expose with xfm2param:
>>
>> #One of 32 transforms
>>
>>> xfm2param input1.xfm
>>>
>> after parameter extraction
>> -center         0.00000    0.00000    0.00000
>> -translation    0.70513    0.30790    0.66079
>> -rotation     -87.58608    4.54388    2.03792
>> -scale          1.00000    1.00000    1.00000
>> -shear         -0.00000   -0.00000    0.00000
>>
>> #Transforms have rotations in range 83-92 -6-7 -2 4
>>
>>> xfmavg *.xfm average.xfm
>>> xfm2param average.xfm
>>>
>> after parameter extraction
>> -center         0.00000    0.00000    0.00000
>> -translation    0.38288    0.50712    0.52295
>> -rotation      -0.04862    0.66666   -0.63100
>> -scale          1.00000    1.00000    1.00000
>> -shear         -0.00000   -0.00000    0.00000
>>
>> #Rotations have been completely lost
>>
>> I just realized this may be due to the values since they?re near -90,
>> could
>> this be a problem?
>> ?
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Thu Feb 11 11:41:23 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 11:41:23 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
Message-ID: <CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>

And the average I get, cause I forgot to include it:

MNI Transform File
%
% Created by xfmavg with a bit of help from octave
%    http://www.octave.org/
%
% Thu Feb 11 10:47:59 EST 2016>>>> xfmavg scan1_01a0_GenericAffine.xfm
scan1_02a0_GenericAffine.xfm scan1_02b0_GenericAffine.xfm
scan1_03a0_GenericAffine.xfm scan1_04a0_GenericAffine.xfm
scan1_05a0_GenericAffine.xfm scan1_05b0_GenericAffine.xfm
scan1_06a0_GenericAffine.xfm scan1_07a0_GenericAffine.xfm
scan1_07b0_GenericAffine.xfm scan1_08b0_GenericAffine.xfm
scan1_10b0_GenericAffine.xfm scan1_11b0_GenericAffine.xfm
scan1_12a0_GenericAffine.xfm scan1_13a0_GenericAffine.xfm
scan1_14a0_GenericAffine.xfm scan1_14b0_GenericAffine.xfm
scan1_16b0_GenericAffine.xfm scan2_01a0_GenericAffine.xfm
scan2_01b0_GenericAffine.xfm scan2_02a0_GenericAffine.xfm
scan2_03a0_GenericAffine.xfm scan2_06a0_GenericAffine.xfm
scan2_06b0_GenericAffine.xfm scan2_08a0_GenericAffine.xfm
scan2_09a0_GenericAffine.xfm scan2_11a0_GenericAffine.xfm
scan3_02a0_GenericAffine.xfm scan3_03a0_GenericAffine.xfm
scan3_07a0_GenericAffine.xfm scan3_09a0_GenericAffine.xfm
scan3_09b0_GenericAffine.xfm average/average.xfm

Transform_Type = Linear;
Linear_Transform =
 9.99871671e-01 1.10030065e-02 1.16437239e-02 3.82880856e-01
 -1.10121374e-02 9.99939105e-01 7.20365393e-04 5.07116829e-01
 -1.16350887e-02 -8.48495237e-04 9.99931950e-01 5.22949707e-01;

?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 11:40 AM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> https://www.dropbox.com/s/vk9zzile5ox7pu4/transforms.tar.bz2?dl=0
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Thu, Feb 11, 2016 at 11:33 AM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com> wrote:
>
>> Maybe it would be easier if you would make all xfms available...
>>
>>
>> On 16-02-11 10:55 AM, Gabriel A. Devenyi wrote:
>>
>>> Sure, easiest to expose with xfm2param:
>>>
>>> #One of 32 transforms
>>>
>>>> xfm2param input1.xfm
>>>>
>>> after parameter extraction
>>> -center         0.00000    0.00000    0.00000
>>> -translation    0.70513    0.30790    0.66079
>>> -rotation     -87.58608    4.54388    2.03792
>>> -scale          1.00000    1.00000    1.00000
>>> -shear         -0.00000   -0.00000    0.00000
>>>
>>> #Transforms have rotations in range 83-92 -6-7 -2 4
>>>
>>>> xfmavg *.xfm average.xfm
>>>> xfm2param average.xfm
>>>>
>>> after parameter extraction
>>> -center         0.00000    0.00000    0.00000
>>> -translation    0.38288    0.50712    0.52295
>>> -rotation      -0.04862    0.66666   -0.63100
>>> -scale          1.00000    1.00000    1.00000
>>> -shear         -0.00000   -0.00000    0.00000
>>>
>>> #Rotations have been completely lost
>>>
>>> I just realized this may be due to the values since they?re near -90,
>>> could
>>> this be a problem?
>>> ?
>>>
>>>
>>
>> --
>> Best regards,
>>
>>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From vladimir.fonov at gmail.com  Thu Feb 11 11:55:26 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Feb 2016 11:55:26 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
Message-ID: <56BCBCFE.6080403@gmail.com>

So, looks like something is broken in octave, or the way how xfmavg 
reads matrices.

I run standard xfmavg and got result
-center         0.00000    0.00000    0.00000
-translation    0.38288    0.50712    0.52295
-rotation      -0.04862    0.66666   -0.63100
-scale          1.00000    1.00000    1.00000
-shear         -0.00000   -0.00000    0.00000

And then run my SciPy based re-implimentation and got following:
-center         0.00000    0.00000    0.00000
-translation    0.37409    0.75399    0.28905
-rotation     -86.85079    2.70359    1.51978
-scale          1.00000    1.00000    1.00000
-shear          0.00000    0.00000    0.00000



The algorithm is the same as in xfmavg - apply matrix logarithm to all 
transforms, perform element-wise averaging, then apply matrix exponent.


On 16-02-11 11:41 AM, Gabriel A. Devenyi wrote:
> And the average I get, cause I forgot to include it:
>
> MNI Transform File
> %
> % Created by xfmavg with a bit of help from octave
> %    http://www.octave.org/
> %
> % Thu Feb 11 10:47:59 EST 2016>>>> xfmavg scan1_01a0_GenericAffine.xfm
> scan1_02a0_GenericAffine.xfm scan1_02b0_GenericAffine.xfm
> scan1_03a0_GenericAffine.xfm scan1_04a0_GenericAffine.xfm
> scan1_05a0_GenericAffine.xfm scan1_05b0_GenericAffine.xfm
> scan1_06a0_GenericAffine.xfm scan1_07a0_GenericAffine.xfm
> scan1_07b0_GenericAffine.xfm scan1_08b0_GenericAffine.xfm
> scan1_10b0_GenericAffine.xfm scan1_11b0_GenericAffine.xfm
> scan1_12a0_GenericAffine.xfm scan1_13a0_GenericAffine.xfm
> scan1_14a0_GenericAffine.xfm scan1_14b0_GenericAffine.xfm
> scan1_16b0_GenericAffine.xfm scan2_01a0_GenericAffine.xfm
> scan2_01b0_GenericAffine.xfm scan2_02a0_GenericAffine.xfm
> scan2_03a0_GenericAffine.xfm scan2_06a0_GenericAffine.xfm
> scan2_06b0_GenericAffine.xfm scan2_08a0_GenericAffine.xfm
> scan2_09a0_GenericAffine.xfm scan2_11a0_GenericAffine.xfm
> scan3_02a0_GenericAffine.xfm scan3_03a0_GenericAffine.xfm
> scan3_07a0_GenericAffine.xfm scan3_09a0_GenericAffine.xfm
> scan3_09b0_GenericAffine.xfm average/average.xfm
>
> Transform_Type = Linear;
> Linear_Transform =
>   9.99871671e-01 1.10030065e-02 1.16437239e-02 3.82880856e-01
>   -1.10121374e-02 9.99939105e-01 7.20365393e-04 5.07116829e-01
>   -1.16350887e-02 -8.48495237e-04 9.99931950e-01 5.22949707e-01;
>
> ?
>


-- 
Best regards,

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

From gdevenyi at gmail.com  Thu Feb 11 12:00:07 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 12:00:07 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <56BCBCFE.6080403@gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
	<56BCBCFE.6080403@gmail.com>
Message-ID: <CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>

This is good to know, CCing in pydpiper guys as this may impact them.

Vlad, would you be willing to share your alternate implementation script?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 11:55 AM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> So, looks like something is broken in octave, or the way how xfmavg reads
> matrices.
>
> I run standard xfmavg and got result
> -center         0.00000    0.00000    0.00000
> -translation    0.38288    0.50712    0.52295
> -rotation      -0.04862    0.66666   -0.63100
> -scale          1.00000    1.00000    1.00000
> -shear         -0.00000   -0.00000    0.00000
>
> And then run my SciPy based re-implimentation and got following:
> -center         0.00000    0.00000    0.00000
> -translation    0.37409    0.75399    0.28905
> -rotation     -86.85079    2.70359    1.51978
> -scale          1.00000    1.00000    1.00000
> -shear          0.00000    0.00000    0.00000
>
>
>
> The algorithm is the same as in xfmavg - apply matrix logarithm to all
> transforms, perform element-wise averaging, then apply matrix exponent.
>
>
>
> On 16-02-11 11:41 AM, Gabriel A. Devenyi wrote:
>
>> And the average I get, cause I forgot to include it:
>>
>> MNI Transform File
>> %
>> % Created by xfmavg with a bit of help from octave
>> %    http://www.octave.org/
>> %
>> % Thu Feb 11 10:47:59 EST 2016>>>> xfmavg scan1_01a0_GenericAffine.xfm
>> scan1_02a0_GenericAffine.xfm scan1_02b0_GenericAffine.xfm
>> scan1_03a0_GenericAffine.xfm scan1_04a0_GenericAffine.xfm
>> scan1_05a0_GenericAffine.xfm scan1_05b0_GenericAffine.xfm
>> scan1_06a0_GenericAffine.xfm scan1_07a0_GenericAffine.xfm
>> scan1_07b0_GenericAffine.xfm scan1_08b0_GenericAffine.xfm
>> scan1_10b0_GenericAffine.xfm scan1_11b0_GenericAffine.xfm
>> scan1_12a0_GenericAffine.xfm scan1_13a0_GenericAffine.xfm
>> scan1_14a0_GenericAffine.xfm scan1_14b0_GenericAffine.xfm
>> scan1_16b0_GenericAffine.xfm scan2_01a0_GenericAffine.xfm
>> scan2_01b0_GenericAffine.xfm scan2_02a0_GenericAffine.xfm
>> scan2_03a0_GenericAffine.xfm scan2_06a0_GenericAffine.xfm
>> scan2_06b0_GenericAffine.xfm scan2_08a0_GenericAffine.xfm
>> scan2_09a0_GenericAffine.xfm scan2_11a0_GenericAffine.xfm
>> scan3_02a0_GenericAffine.xfm scan3_03a0_GenericAffine.xfm
>> scan3_07a0_GenericAffine.xfm scan3_09a0_GenericAffine.xfm
>> scan3_09b0_GenericAffine.xfm average/average.xfm
>>
>> Transform_Type = Linear;
>> Linear_Transform =
>>   9.99871671e-01 1.10030065e-02 1.16437239e-02 3.82880856e-01
>>   -1.10121374e-02 9.99939105e-01 7.20365393e-04 5.07116829e-01
>>   -1.16350887e-02 -8.48495237e-04 9.99931950e-01 5.22949707e-01;
>>
>> ?
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Thu Feb 11 13:15:33 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Feb 2016 13:15:33 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
	<56BCBCFE.6080403@gmail.com>
	<CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>
Message-ID: <CAMCwi7MHSP=+L4rG3vYFuec938pY0BzeqtGj9k7S2pUAASAdyw@mail.gmail.com>

Ok, here it is :
https://github.com/BIC-MNI/pyezminc/blob/develop/examples/xfmavg_scipy.py

Note - it needs to have develop branch of pyezminc to be installed.

On Thu, Feb 11, 2016 at 12:00 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> This is good to know, CCing in pydpiper guys as this may impact them.
>
> Vlad, would you be willing to share your alternate implementation script?
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Thu, Feb 11, 2016 at 11:55 AM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com> wrote:
>
> > So, looks like something is broken in octave, or the way how xfmavg reads
> > matrices.
> >
> > I run standard xfmavg and got result
> > -center         0.00000    0.00000    0.00000
> > -translation    0.38288    0.50712    0.52295
> > -rotation      -0.04862    0.66666   -0.63100
> > -scale          1.00000    1.00000    1.00000
> > -shear         -0.00000   -0.00000    0.00000
> >
> > And then run my SciPy based re-implimentation and got following:
> > -center         0.00000    0.00000    0.00000
> > -translation    0.37409    0.75399    0.28905
> > -rotation     -86.85079    2.70359    1.51978
> > -scale          1.00000    1.00000    1.00000
> > -shear          0.00000    0.00000    0.00000
> >
> >
> >
> > The algorithm is the same as in xfmavg - apply matrix logarithm to all
> > transforms, perform element-wise averaging, then apply matrix exponent.
> >
> >
> >
> > On 16-02-11 11:41 AM, Gabriel A. Devenyi wrote:
> >
> >> And the average I get, cause I forgot to include it:
> >>
> >> MNI Transform File
> >> %
> >> % Created by xfmavg with a bit of help from octave
> >> %    http://www.octave.org/
> >> %
> >> % Thu Feb 11 10:47:59 EST 2016>>>> xfmavg scan1_01a0_GenericAffine.xfm
> >> scan1_02a0_GenericAffine.xfm scan1_02b0_GenericAffine.xfm
> >> scan1_03a0_GenericAffine.xfm scan1_04a0_GenericAffine.xfm
> >> scan1_05a0_GenericAffine.xfm scan1_05b0_GenericAffine.xfm
> >> scan1_06a0_GenericAffine.xfm scan1_07a0_GenericAffine.xfm
> >> scan1_07b0_GenericAffine.xfm scan1_08b0_GenericAffine.xfm
> >> scan1_10b0_GenericAffine.xfm scan1_11b0_GenericAffine.xfm
> >> scan1_12a0_GenericAffine.xfm scan1_13a0_GenericAffine.xfm
> >> scan1_14a0_GenericAffine.xfm scan1_14b0_GenericAffine.xfm
> >> scan1_16b0_GenericAffine.xfm scan2_01a0_GenericAffine.xfm
> >> scan2_01b0_GenericAffine.xfm scan2_02a0_GenericAffine.xfm
> >> scan2_03a0_GenericAffine.xfm scan2_06a0_GenericAffine.xfm
> >> scan2_06b0_GenericAffine.xfm scan2_08a0_GenericAffine.xfm
> >> scan2_09a0_GenericAffine.xfm scan2_11a0_GenericAffine.xfm
> >> scan3_02a0_GenericAffine.xfm scan3_03a0_GenericAffine.xfm
> >> scan3_07a0_GenericAffine.xfm scan3_09a0_GenericAffine.xfm
> >> scan3_09b0_GenericAffine.xfm average/average.xfm
> >>
> >> Transform_Type = Linear;
> >> Linear_Transform =
> >>   9.99871671e-01 1.10030065e-02 1.16437239e-02 3.82880856e-01
> >>   -1.10121374e-02 9.99939105e-01 7.20365393e-04 5.07116829e-01
> >>   -1.16350887e-02 -8.48495237e-04 9.99931950e-01 5.22949707e-01;
> >>
> >> ?
> >>
> >>
> >
> > --
> > Best regards,
> >
> >  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.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

From gdevenyi at gmail.com  Thu Feb 11 13:22:17 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 13:22:17 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAMCwi7MHSP=+L4rG3vYFuec938pY0BzeqtGj9k7S2pUAASAdyw@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
	<56BCBCFE.6080403@gmail.com>
	<CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>
	<CAMCwi7MHSP=+L4rG3vYFuec938pY0BzeqtGj9k7S2pUAASAdyw@mail.gmail.com>
Message-ID: <CAFQOoOo-71Vdva8stfKewsufRYu43+r4EJkTr3uUj7rskNhWDg@mail.gmail.com>

Thanks Vlad,

To be clear, not pyezminc isn't currently included in any minc-toolkit?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 1:15 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Ok, here it is :
> https://github.com/BIC-MNI/pyezminc/blob/develop/examples/xfmavg_scipy.py
>
> Note - it needs to have develop branch of pyezminc to be installed.
>
> On Thu, Feb 11, 2016 at 12:00 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
> > This is good to know, CCing in pydpiper guys as this may impact them.
> >
> > Vlad, would you be willing to share your alternate implementation script?
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> >
> > On Thu, Feb 11, 2016 at 11:55 AM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com> wrote:
> >
> > > So, looks like something is broken in octave, or the way how xfmavg
> reads
> > > matrices.
> > >
> > > I run standard xfmavg and got result
> > > -center         0.00000    0.00000    0.00000
> > > -translation    0.38288    0.50712    0.52295
> > > -rotation      -0.04862    0.66666   -0.63100
> > > -scale          1.00000    1.00000    1.00000
> > > -shear         -0.00000   -0.00000    0.00000
> > >
> > > And then run my SciPy based re-implimentation and got following:
> > > -center         0.00000    0.00000    0.00000
> > > -translation    0.37409    0.75399    0.28905
> > > -rotation     -86.85079    2.70359    1.51978
> > > -scale          1.00000    1.00000    1.00000
> > > -shear          0.00000    0.00000    0.00000
> > >
> > >
> > >
> > > The algorithm is the same as in xfmavg - apply matrix logarithm to all
> > > transforms, perform element-wise averaging, then apply matrix exponent.
> > >
> > >
> > >
> > > On 16-02-11 11:41 AM, Gabriel A. Devenyi wrote:
> > >
> > >> And the average I get, cause I forgot to include it:
> > >>
> > >> MNI Transform File
> > >> %
> > >> % Created by xfmavg with a bit of help from octave
> > >> %    http://www.octave.org/
> > >> %
> > >> % Thu Feb 11 10:47:59 EST 2016>>>> xfmavg scan1_01a0_GenericAffine.xfm
> > >> scan1_02a0_GenericAffine.xfm scan1_02b0_GenericAffine.xfm
> > >> scan1_03a0_GenericAffine.xfm scan1_04a0_GenericAffine.xfm
> > >> scan1_05a0_GenericAffine.xfm scan1_05b0_GenericAffine.xfm
> > >> scan1_06a0_GenericAffine.xfm scan1_07a0_GenericAffine.xfm
> > >> scan1_07b0_GenericAffine.xfm scan1_08b0_GenericAffine.xfm
> > >> scan1_10b0_GenericAffine.xfm scan1_11b0_GenericAffine.xfm
> > >> scan1_12a0_GenericAffine.xfm scan1_13a0_GenericAffine.xfm
> > >> scan1_14a0_GenericAffine.xfm scan1_14b0_GenericAffine.xfm
> > >> scan1_16b0_GenericAffine.xfm scan2_01a0_GenericAffine.xfm
> > >> scan2_01b0_GenericAffine.xfm scan2_02a0_GenericAffine.xfm
> > >> scan2_03a0_GenericAffine.xfm scan2_06a0_GenericAffine.xfm
> > >> scan2_06b0_GenericAffine.xfm scan2_08a0_GenericAffine.xfm
> > >> scan2_09a0_GenericAffine.xfm scan2_11a0_GenericAffine.xfm
> > >> scan3_02a0_GenericAffine.xfm scan3_03a0_GenericAffine.xfm
> > >> scan3_07a0_GenericAffine.xfm scan3_09a0_GenericAffine.xfm
> > >> scan3_09b0_GenericAffine.xfm average/average.xfm
> > >>
> > >> Transform_Type = Linear;
> > >> Linear_Transform =
> > >>   9.99871671e-01 1.10030065e-02 1.16437239e-02 3.82880856e-01
> > >>   -1.10121374e-02 9.99939105e-01 7.20365393e-04 5.07116829e-01
> > >>   -1.16350887e-02 -8.48495237e-04 9.99931950e-01 5.22949707e-01;
> > >>
> > >> ?
> > >>
> > >>
> > >
> > > --
> > > Best regards,
> > >
> > >  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Thu Feb 11 13:25:57 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 11 Feb 2016 13:25:57 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <CAFQOoOo-71Vdva8stfKewsufRYu43+r4EJkTr3uUj7rskNhWDg@mail.gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
	<56BCBCFE.6080403@gmail.com>
	<CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>
	<CAMCwi7MHSP=+L4rG3vYFuec938pY0BzeqtGj9k7S2pUAASAdyw@mail.gmail.com>
	<CAFQOoOo-71Vdva8stfKewsufRYu43+r4EJkTr3uUj7rskNhWDg@mail.gmail.com>
Message-ID: <56BCD235.9000203@gmail.com>

On 16-02-11 01:22 PM, Gabriel A. Devenyi wrote:
> Thanks Vlad,
>
> To be clear, not pyezminc isn't currently included in any minc-toolkit?
>

pyezminc is not included


-- 
Best regards,

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

From gdevenyi at gmail.com  Thu Feb 11 13:30:38 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 11 Feb 2016 13:30:38 -0500
Subject: [MINC-users] xfmavg and lsq6 transforms
In-Reply-To: <56BCD235.9000203@gmail.com>
References: <CAFQOoOqWqzvmJ6y4vhQirG1ShfubTcL7k1RfN2NmsJRiBvhCzA@mail.gmail.com>
	<CAMCwi7PcUBxSyH=PnBCVqBT8-jbmXwkgFnnKKpE+udfvjn0q=A@mail.gmail.com>
	<CAFQOoOqyKSiyKVz4E53Ky52ktWKiN+SLeFqBSEKdLePuOumCaQ@mail.gmail.com>
	<56BCB7C9.1090502@gmail.com>
	<CAFQOoOqkh7=JRXsuNsN+Wis8HkCctaocJG328XSf4mdN1ZoCXw@mail.gmail.com>
	<CAFQOoOpc1FgZnUyMoxupUAc7Oji53cSiK4PBYeuiuV-oXF3Kjw@mail.gmail.com>
	<56BCBCFE.6080403@gmail.com>
	<CAFQOoOosPGACWzAveUQTngRh0eMj_1MqC0a6Y9BEudTf-qw2Pg@mail.gmail.com>
	<CAMCwi7MHSP=+L4rG3vYFuec938pY0BzeqtGj9k7S2pUAASAdyw@mail.gmail.com>
	<CAFQOoOo-71Vdva8stfKewsufRYu43+r4EJkTr3uUj7rskNhWDg@mail.gmail.com>
	<56BCD235.9000203@gmail.com>
Message-ID: <CAFQOoOqX=Q1_EzaR9C5DPPV3XWe_gBaELzUavzZ394x++s80Ag@mail.gmail.com>

Develop branch installs against 1.9.11 and script works as expected.

Thanks!

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Thu, Feb 11, 2016 at 1:25 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> On 16-02-11 01:22 PM, Gabriel A. Devenyi wrote:
>
>> Thanks Vlad,
>>
>> To be clear, not pyezminc isn't currently included in any minc-toolkit?
>>
>>
> pyezminc is not included
>
>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From robert.d.vincent at mcgill.ca  Thu Feb 11 14:34:37 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Thu, 11 Feb 2016 14:34:37 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
Message-ID: <CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>

Hi Alex,

I just pushed a fix to Github that should put correct Z axis spacing in
these sequences.

    -bert

On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Just a follwup, the "newer" dicom creator is dcm2niix, may be able to find
> some useful info here https://github.com/neurolabusc/dcm2niix
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Alex,
> >
> > We've encountered so little 3D DICOM over the years I'm not surprised it
> > isn't handled well.
> >
> > Thanks for the dataset. I will look into it and let you know.
> >
> >     -bert
> >
> >
> > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <zijdenbos at gmail.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > I got some 3D DICOM SPECT data that dcm2mnc issues with - depending on
> > what
> > > version of dcm2mnc I use, I get somewhat different results; but in most
> > > cases I end up with irregular z-spacing and/or a flipped z-axis. The
> most
> > > recent version I tried was dcm2mnc version 2.01.03 from minc-toolkit
> > > version 1.0.08.
> > >
> > > If I run the same thing through dcm2nii followed by nii2mnc (ugh!), I
> > > actually get a volume that looks like I expected. There appears to be
> > > coordinate space information in the 3D DICOM that dcm2nii seems to be
> > able
> > > to interpret, but dcm2mnc does not.
> > >
> > > Thoughts/pointers/updated versions of dcm2mnc?
> > >
> > > Here is a sample DICOM set:
> > > ?
> > >  s1_0013006_3006.dcm.gz
> > > <
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > >
> > > ?
> > >
> > > Thanks,
> > >
> > > -- A
> > > _______________________________________________
> > > 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
>

From zijdenbos at gmail.com  Thu Feb 11 15:02:38 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 11 Feb 2016 15:02:38 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
	<CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
Message-ID: <CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>

Hi Bert,

Cool - thanks much! The steps/zspace now look good :-)

However I believe that the starts may still be wrong. When run through
dcm2nii - nii2mnc, the volume ends up with start values that I suspect are
'real' (they roughly match the corresponding T1 that I have). With this new
dcm2mnc, the start values are all 0.

-- A

On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Alex,
>
> I just pushed a fix to Github that should put correct Z axis spacing in
> these sequences.
>
>     -bert
>
> On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
> > Just a follwup, the "newer" dicom creator is dcm2niix, may be able to
> find
> > some useful info here https://github.com/neurolabusc/dcm2niix
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> >
> > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > robert.d.vincent at mcgill.ca> wrote:
> >
> > > Hi Alex,
> > >
> > > We've encountered so little 3D DICOM over the years I'm not surprised
> it
> > > isn't handled well.
> > >
> > > Thanks for the dataset. I will look into it and let you know.
> > >
> > >     -bert
> > >
> > >
> > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <zijdenbos at gmail.com>
> > > wrote:
> > >
> > > > Hi all,
> > > >
> > > > I got some 3D DICOM SPECT data that dcm2mnc issues with - depending
> on
> > > what
> > > > version of dcm2mnc I use, I get somewhat different results; but in
> most
> > > > cases I end up with irregular z-spacing and/or a flipped z-axis. The
> > most
> > > > recent version I tried was dcm2mnc version 2.01.03 from minc-toolkit
> > > > version 1.0.08.
> > > >
> > > > If I run the same thing through dcm2nii followed by nii2mnc (ugh!), I
> > > > actually get a volume that looks like I expected. There appears to be
> > > > coordinate space information in the 3D DICOM that dcm2nii seems to be
> > > able
> > > > to interpret, but dcm2mnc does not.
> > > >
> > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > >
> > > > Here is a sample DICOM set:
> > > > ?
> > > >  s1_0013006_3006.dcm.gz
> > > > <
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > >
> > > > ?
> > > >
> > > > Thanks,
> > > >
> > > > -- A
> > > > _______________________________________________
> > > > 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From robert.d.vincent at mcgill.ca  Thu Feb 11 15:43:19 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Thu, 11 Feb 2016 15:43:19 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
	<CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
	<CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>
Message-ID: <CAAd5DeRWWWa92LFWSvLdmV1c3dap6iEAyQ6sokRKkZbdqM539w@mail.gmail.com>

Hi Alex,

That is surprising. There is only one position indicated in the file, and
we are correctly reading it as 0, 0, 0 (it's a DICOM element 0020, 0032).
So as far as we are concerned we're assigning the correct start values.

It's possible that dcm2nii is "inventing" position values corresponding to
the centre of the grid - are they something like 150.6? (128/2)*2.353

    -bert


On Thu, Feb 11, 2016 at 3:02 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Bert,
>
> Cool - thanks much! The steps/zspace now look good :-)
>
> However I believe that the starts may still be wrong. When run through
> dcm2nii - nii2mnc, the volume ends up with start values that I suspect are
> 'real' (they roughly match the corresponding T1 that I have). With this new
> dcm2mnc, the start values are all 0.
>
> -- A
>
> On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Alex,
> >
> > I just pushed a fix to Github that should put correct Z axis spacing in
> > these sequences.
> >
> >     -bert
> >
> > On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <gdevenyi at gmail.com
> >
> > wrote:
> >
> > > Just a follwup, the "newer" dicom creator is dcm2niix, may be able to
> > find
> > > some useful info here https://github.com/neurolabusc/dcm2niix
> > >
> > > --
> > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > Research Computing Associate
> > > Computational Brain Anatomy Laboratory
> > > Cerebral Imaging Center
> > > Douglas Mental Health University Institute
> > > McGill University
> > > t: 514.761.6131x4781
> > > e: gdevenyi at gmail.com
> > >
> > > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > > robert.d.vincent at mcgill.ca> wrote:
> > >
> > > > Hi Alex,
> > > >
> > > > We've encountered so little 3D DICOM over the years I'm not surprised
> > it
> > > > isn't handled well.
> > > >
> > > > Thanks for the dataset. I will look into it and let you know.
> > > >
> > > >     -bert
> > > >
> > > >
> > > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <
> zijdenbos at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I got some 3D DICOM SPECT data that dcm2mnc issues with - depending
> > on
> > > > what
> > > > > version of dcm2mnc I use, I get somewhat different results; but in
> > most
> > > > > cases I end up with irregular z-spacing and/or a flipped z-axis.
> The
> > > most
> > > > > recent version I tried was dcm2mnc version 2.01.03 from
> minc-toolkit
> > > > > version 1.0.08.
> > > > >
> > > > > If I run the same thing through dcm2nii followed by nii2mnc
> (ugh!), I
> > > > > actually get a volume that looks like I expected. There appears to
> be
> > > > > coordinate space information in the 3D DICOM that dcm2nii seems to
> be
> > > > able
> > > > > to interpret, but dcm2mnc does not.
> > > > >
> > > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > > >
> > > > > Here is a sample DICOM set:
> > > > > ?
> > > > >  s1_0013006_3006.dcm.gz
> > > > > <
> > > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > > >
> > > > > ?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > -- A
> > > > > _______________________________________________
> > > > > 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
> > >
> > _______________________________________________
> > 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 zijdenbos at gmail.com  Thu Feb 11 15:59:28 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 11 Feb 2016 15:59:28 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CAAd5DeRWWWa92LFWSvLdmV1c3dap6iEAyQ6sokRKkZbdqM539w@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
	<CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
	<CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>
	<CAAd5DeRWWWa92LFWSvLdmV1c3dap6iEAyQ6sokRKkZbdqM539w@mail.gmail.com>
Message-ID: <CABEEk142kmx3WPUzdfYgBzYEC40JxoWMLD-OPfbfwVA6Y7WT0w@mail.gmail.com>

Hi Bert,

Yes - converting to nii and then to MINC yields this volume:

image: signed__ short 0 to 32766
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     65        3.138     -101.985
    yspace                    128        2.353     -150.592
    xspace                    128        2.353     -150.592

So I suspect you are right... Either way is fine with me in practice, I
just wanted to make sure the conversion wasn't dropping information.

Thanks!

-- A


On Thu, Feb 11, 2016 at 3:43 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Alex,
>
> That is surprising. There is only one position indicated in the file, and
> we are correctly reading it as 0, 0, 0 (it's a DICOM element 0020, 0032).
> So as far as we are concerned we're assigning the correct start values.
>
> It's possible that dcm2nii is "inventing" position values corresponding to
> the centre of the grid - are they something like 150.6? (128/2)*2.353
>
>     -bert
>
>
> On Thu, Feb 11, 2016 at 3:02 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi Bert,
> >
> > Cool - thanks much! The steps/zspace now look good :-)
> >
> > However I believe that the starts may still be wrong. When run through
> > dcm2nii - nii2mnc, the volume ends up with start values that I suspect
> are
> > 'real' (they roughly match the corresponding T1 that I have). With this
> new
> > dcm2mnc, the start values are all 0.
> >
> > -- A
> >
> > On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
> > robert.d.vincent at mcgill.ca> wrote:
> >
> > > Hi Alex,
> > >
> > > I just pushed a fix to Github that should put correct Z axis spacing in
> > > these sequences.
> > >
> > >     -bert
> > >
> > > On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <
> gdevenyi at gmail.com
> > >
> > > wrote:
> > >
> > > > Just a follwup, the "newer" dicom creator is dcm2niix, may be able to
> > > find
> > > > some useful info here https://github.com/neurolabusc/dcm2niix
> > > >
> > > > --
> > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > Research Computing Associate
> > > > Computational Brain Anatomy Laboratory
> > > > Cerebral Imaging Center
> > > > Douglas Mental Health University Institute
> > > > McGill University
> > > > t: 514.761.6131x4781
> > > > e: gdevenyi at gmail.com
> > > >
> > > > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > > > robert.d.vincent at mcgill.ca> wrote:
> > > >
> > > > > Hi Alex,
> > > > >
> > > > > We've encountered so little 3D DICOM over the years I'm not
> surprised
> > > it
> > > > > isn't handled well.
> > > > >
> > > > > Thanks for the dataset. I will look into it and let you know.
> > > > >
> > > > >     -bert
> > > > >
> > > > >
> > > > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <
> > zijdenbos at gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I got some 3D DICOM SPECT data that dcm2mnc issues with -
> depending
> > > on
> > > > > what
> > > > > > version of dcm2mnc I use, I get somewhat different results; but
> in
> > > most
> > > > > > cases I end up with irregular z-spacing and/or a flipped z-axis.
> > The
> > > > most
> > > > > > recent version I tried was dcm2mnc version 2.01.03 from
> > minc-toolkit
> > > > > > version 1.0.08.
> > > > > >
> > > > > > If I run the same thing through dcm2nii followed by nii2mnc
> > (ugh!), I
> > > > > > actually get a volume that looks like I expected. There appears
> to
> > be
> > > > > > coordinate space information in the 3D DICOM that dcm2nii seems
> to
> > be
> > > > > able
> > > > > > to interpret, but dcm2mnc does not.
> > > > > >
> > > > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > > > >
> > > > > > Here is a sample DICOM set:
> > > > > > ?
> > > > > >  s1_0013006_3006.dcm.gz
> > > > > > <
> > > > > >
> > > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > > > >
> > > > > > ?
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > -- A
> > > > > > _______________________________________________
> > > > > > 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
> > > >
> > > _______________________________________________
> > > 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
>

From robert.d.vincent at mcgill.ca  Thu Feb 11 16:11:36 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Thu, 11 Feb 2016 16:11:36 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CABEEk142kmx3WPUzdfYgBzYEC40JxoWMLD-OPfbfwVA6Y7WT0w@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
	<CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
	<CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>
	<CAAd5DeRWWWa92LFWSvLdmV1c3dap6iEAyQ6sokRKkZbdqM539w@mail.gmail.com>
	<CABEEk142kmx3WPUzdfYgBzYEC40JxoWMLD-OPfbfwVA6Y7WT0w@mail.gmail.com>
Message-ID: <CAAd5DeS-+SEojeWPai0YWFk7wNyMMDxUk=ojXd5YdXyq-qSxvA@mail.gmail.com>

Hi Alex,

I'll try to double check our handling of this. It could be that some other
field in the DICOM is instructing that the position should be treated as a
centre rather than an corner. But my understanding has always been that the
position is relative to the upper left hand corner of the image.

It's likely that the dcm2nii developers implemented a kludge for a zero
position. If you think it's worth it, we could certainly do the same.

    -bert

On Thu, Feb 11, 2016 at 3:59 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Bert,
>
> Yes - converting to nii and then to MINC yields this volume:
>
> image: signed__ short 0 to 32766
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                     65        3.138     -101.985
>     yspace                    128        2.353     -150.592
>     xspace                    128        2.353     -150.592
>
> So I suspect you are right... Either way is fine with me in practice, I
> just wanted to make sure the conversion wasn't dropping information.
>
> Thanks!
>
> -- A
>
>
> On Thu, Feb 11, 2016 at 3:43 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Alex,
> >
> > That is surprising. There is only one position indicated in the file, and
> > we are correctly reading it as 0, 0, 0 (it's a DICOM element 0020, 0032).
> > So as far as we are concerned we're assigning the correct start values.
> >
> > It's possible that dcm2nii is "inventing" position values corresponding
> to
> > the centre of the grid - are they something like 150.6? (128/2)*2.353
> >
> >     -bert
> >
> >
> > On Thu, Feb 11, 2016 at 3:02 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > wrote:
> >
> > > Hi Bert,
> > >
> > > Cool - thanks much! The steps/zspace now look good :-)
> > >
> > > However I believe that the starts may still be wrong. When run through
> > > dcm2nii - nii2mnc, the volume ends up with start values that I suspect
> > are
> > > 'real' (they roughly match the corresponding T1 that I have). With this
> > new
> > > dcm2mnc, the start values are all 0.
> > >
> > > -- A
> > >
> > > On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
> > > robert.d.vincent at mcgill.ca> wrote:
> > >
> > > > Hi Alex,
> > > >
> > > > I just pushed a fix to Github that should put correct Z axis spacing
> in
> > > > these sequences.
> > > >
> > > >     -bert
> > > >
> > > > On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <
> > gdevenyi at gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > Just a follwup, the "newer" dicom creator is dcm2niix, may be able
> to
> > > > find
> > > > > some useful info here https://github.com/neurolabusc/dcm2niix
> > > > >
> > > > > --
> > > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > > Research Computing Associate
> > > > > Computational Brain Anatomy Laboratory
> > > > > Cerebral Imaging Center
> > > > > Douglas Mental Health University Institute
> > > > > McGill University
> > > > > t: 514.761.6131x4781
> > > > > e: gdevenyi at gmail.com
> > > > >
> > > > > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > > > > robert.d.vincent at mcgill.ca> wrote:
> > > > >
> > > > > > Hi Alex,
> > > > > >
> > > > > > We've encountered so little 3D DICOM over the years I'm not
> > surprised
> > > > it
> > > > > > isn't handled well.
> > > > > >
> > > > > > Thanks for the dataset. I will look into it and let you know.
> > > > > >
> > > > > >     -bert
> > > > > >
> > > > > >
> > > > > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <
> > > zijdenbos at gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi all,
> > > > > > >
> > > > > > > I got some 3D DICOM SPECT data that dcm2mnc issues with -
> > depending
> > > > on
> > > > > > what
> > > > > > > version of dcm2mnc I use, I get somewhat different results; but
> > in
> > > > most
> > > > > > > cases I end up with irregular z-spacing and/or a flipped
> z-axis.
> > > The
> > > > > most
> > > > > > > recent version I tried was dcm2mnc version 2.01.03 from
> > > minc-toolkit
> > > > > > > version 1.0.08.
> > > > > > >
> > > > > > > If I run the same thing through dcm2nii followed by nii2mnc
> > > (ugh!), I
> > > > > > > actually get a volume that looks like I expected. There appears
> > to
> > > be
> > > > > > > coordinate space information in the 3D DICOM that dcm2nii seems
> > to
> > > be
> > > > > > able
> > > > > > > to interpret, but dcm2mnc does not.
> > > > > > >
> > > > > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > > > > >
> > > > > > > Here is a sample DICOM set:
> > > > > > > ?
> > > > > > >  s1_0013006_3006.dcm.gz
> > > > > > > <
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > > > > >
> > > > > > > ?
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > -- A
> > > > > > > _______________________________________________
> > > > > > > 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
> > > > >
> > > > _______________________________________________
> > > > 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From redoute at cermep.fr  Fri Feb 12 04:39:55 2016
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Fri, 12 Feb 2016 10:39:55 +0100
Subject: [MINC-users] new release of minc-toolkit
In-Reply-To: <56BB62EE.1000708@gmail.com>
References: <56BB62EE.1000708@gmail.com>
Message-ID: <56BDA86B.4040701@cermep.fr>

Thank you for this new release!

I have a problem with the mnc2nii function:

1: convertion of Dynamic PET data from DICOM to MINC with dcm2mnc is OK
2: PET_DYN.mnc to PET_DYN.nii with mnc2nii is OK

but

if I make an average file of my PET_DYN with mincaverage -avgdim time
and then

mnc2nii PET_DYN_avg.mnc PET_DYN_avg.nii

It crashes with:

> *** Error in `mnc2nii': munmap_chunk(): invalid pointer: 
> 0x000000000090cb50 ***

thanks for your help

Jerome




Le 10/02/2016 17:18, Vladimir S. FONOV a ?crit :
> Hello Everybody,
>
>
> I made a new release of minc-toolkit, standard branch - version 1.0.08 
> and v2 branch - version 1.9.11.  It includes all the latest versions 
> of minc tools (as of 2nd of February 2016). V2 branch includes ITK 4.9 
> library and latest versions of ANTs and Elastix. V2 branch now also 
> includes tools for patch-based segmentations ( see 
> https://github.com/vfonov/patch_morphology ).
>
> MacOSX version was updated to work properly on 10.11 ( El Capitan). 
> Unfortunately I was not able to build v2 branch for older (10.7) 
> version, so only the standard branch is available to folks who are 
> stuck with old version of MacOS X.
>
> All the binary packages are downloadable from 
> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit
>
>
> Note that web page http://www.mcgill.ca/bic/software/minc/minctoolkit 
> is out of date!


-- 
==================================================================
J?r?me Redout?
Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
CERMEP - Imagerie du vivant
59 Bd Pinel. 69677 Bron - FRANCE
tel : 33 (0)4 72 68 86 18 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
==================================================================



From robert.d.vincent at mcgill.ca  Fri Feb 12 09:28:05 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Fri, 12 Feb 2016 09:28:05 -0500
Subject: [MINC-users] new release of minc-toolkit
In-Reply-To: <56BDA86B.4040701@cermep.fr>
References: <56BB62EE.1000708@gmail.com> <56BDA86B.4040701@cermep.fr>
Message-ID: <CAAd5DeTkJaW6o7HagUHOFqe4GxJcGF0A4FkOiKJL54tZ==NpTA@mail.gmail.com>

Hi J?r?me,

Thank you for the report - I'll look into it.

    -bert

On Fri, Feb 12, 2016 at 4:39 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Thank you for this new release!
>
> I have a problem with the mnc2nii function:
>
> 1: convertion of Dynamic PET data from DICOM to MINC with dcm2mnc is OK
> 2: PET_DYN.mnc to PET_DYN.nii with mnc2nii is OK
>
> but
>
> if I make an average file of my PET_DYN with mincaverage -avgdim time
> and then
>
> mnc2nii PET_DYN_avg.mnc PET_DYN_avg.nii
>
> It crashes with:
>
> *** Error in `mnc2nii': munmap_chunk(): invalid pointer:
>> 0x000000000090cb50 ***
>>
>
> thanks for your help
>
> Jerome
>
>
>
>
> Le 10/02/2016 17:18, Vladimir S. FONOV a ?crit :
>
>> Hello Everybody,
>>
>>
>> I made a new release of minc-toolkit, standard branch - version 1.0.08
>> and v2 branch - version 1.9.11.  It includes all the latest versions of
>> minc tools (as of 2nd of February 2016). V2 branch includes ITK 4.9 library
>> and latest versions of ANTs and Elastix. V2 branch now also includes tools
>> for patch-based segmentations ( see
>> https://github.com/vfonov/patch_morphology ).
>>
>> MacOSX version was updated to work properly on 10.11 ( El Capitan).
>> Unfortunately I was not able to build v2 branch for older (10.7) version,
>> so only the standard branch is available to folks who are stuck with old
>> version of MacOS X.
>>
>> All the binary packages are downloadable from
>> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit
>>
>>
>> Note that web page http://www.mcgill.ca/bic/software/minc/minctoolkit is
>> out of date!
>>
>
>
> --
> ==================================================================
> J?r?me Redout?
> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
> CERMEP - Imagerie du vivant
> 59 Bd Pinel. 69677 Bron - FRANCE
> tel : 33 (0)4 72 68 86 18 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================================
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Mon Feb 15 00:53:23 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 15 Feb 2016 15:53:23 +1000
Subject: [MINC-users] MINC-users Digest, Vol 126, Issue 2
In-Reply-To: <CAH7=K=X=WZ6HaKBWi3dEjSBh=KntdM8JzCjxe6zcoiKeQaBc4Q@mail.gmail.com>
References: <mailman.7.1455123602.7511.minc-users@bic.mni.mcgill.ca>
	<CAH7=K=X=WZ6HaKBWi3dEjSBh=KntdM8JzCjxe6zcoiKeQaBc4Q@mail.gmail.com>
Message-ID: <CAG0CB22Lo+PFRRJyqBNruKkA0oiFFOMRUwQ+WvLgMFx2Jmd0jA@mail.gmail.com>

Hi,

Have a look at the classify package that is part of minc-toolkit. A
typical invocation is as such:

    classify_clean \
         -tagdir /opt/minc-itk4/share/classify \
         -tag_transform <linear_transform_to_mni_space.xfm> \
         input.mnc classified.mnc

Note that for this to work you will have to first estimate a linear
transformation to MNI/ICBM space using the mritotal tool.


a


On 12 February 2016 at 02:18, Hemanth I (Hemambaradarahara   Rao)
<hihemanth08 at gmail.com> wrote:
> Hii minc -users,
> I am using minc format brain images for wavelet based image fusion.
> Can i use this tool kit for image segmentation if possible can anybody
> explain how to use this toolkit for image segmentation.
> I am using both ubuntu 14.04 and windows 8.1 so tool kits in ubuntu or
> windows both i can use.if anyone know about image segmentation for minc
> images using these tool kits please do respond it will be helpful for me.

From zijdenbos at gmail.com  Mon Feb 15 12:29:34 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 15 Feb 2016 12:29:34 -0500
Subject: [MINC-users] dcm2mnc vs 3D DICOM
In-Reply-To: <CAAd5DeS-+SEojeWPai0YWFk7wNyMMDxUk=ojXd5YdXyq-qSxvA@mail.gmail.com>
References: <CABEEk179H2Zq0Vcs_EBgxaUKL9rrzkykXvcym6QZtWfV-8ftPw@mail.gmail.com>
	<CAAd5DeTwUpU4N4QAQaxc5_mPrvwCTkLd4vKAq-3iBkoyvSbAcw@mail.gmail.com>
	<CAFQOoOqhfMUYca0jY14GnhX7j5UzubBUn+L2vsCLmt3GmJ2Wmg@mail.gmail.com>
	<CAAd5DeRUd6RE5d5TyEisyHi_rAL2B4krwBbn=8qK1whs-mcstA@mail.gmail.com>
	<CABEEk1795KR3kJoe0K8UmwtjuSDs0J8nr95xP9C=Ws4+MGSeLg@mail.gmail.com>
	<CAAd5DeRWWWa92LFWSvLdmV1c3dap6iEAyQ6sokRKkZbdqM539w@mail.gmail.com>
	<CABEEk142kmx3WPUzdfYgBzYEC40JxoWMLD-OPfbfwVA6Y7WT0w@mail.gmail.com>
	<CAAd5DeS-+SEojeWPai0YWFk7wNyMMDxUk=ojXd5YdXyq-qSxvA@mail.gmail.com>
Message-ID: <CABEEk15qhzEdFwJK5SeoXBbOg5j5URC=teQTDtWm3PqmWowZ=Q@mail.gmail.com>

Hi Bert,

I have admit I don't have a strong preference one way or the other. If the
DICOM reports a scanner-world-coordinate origin (0,0,0), it probably means
that the 'real' coordinate information was lost or never existed (e.g.,
data was processed). In that case it probably doesn't matter as any further
processing would need explicit registration anyways. I can imagine that,
when unknown, placing the world coordinate origin in the center of the
image, as dcm2nii appears to do, is a practical choice, but not really
better than using (0,0,0) that the DICOM actually reports. Only advantage I
can think of is that it brings native volumes up seeming better aligned
with other modalities. It's pretty trivial to shift the starts to another
location after the fact anyways.

I don't know if anybody else has opinions about this, but AFAIC we can
leave this as-is.

-- A

On Thu, Feb 11, 2016 at 4:11 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Alex,
>
> I'll try to double check our handling of this. It could be that some other
> field in the DICOM is instructing that the position should be treated as a
> centre rather than an corner. But my understanding has always been that the
> position is relative to the upper left hand corner of the image.
>
> It's likely that the dcm2nii developers implemented a kludge for a zero
> position. If you think it's worth it, we could certainly do the same.
>
>     -bert
>
> On Thu, Feb 11, 2016 at 3:59 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi Bert,
> >
> > Yes - converting to nii and then to MINC yields this volume:
> >
> > image: signed__ short 0 to 32766
> > image dimensions: zspace yspace xspace
> >     dimension name         length         step        start
> >     --------------         ------         ----        -----
> >     zspace                     65        3.138     -101.985
> >     yspace                    128        2.353     -150.592
> >     xspace                    128        2.353     -150.592
> >
> > So I suspect you are right... Either way is fine with me in practice, I
> > just wanted to make sure the conversion wasn't dropping information.
> >
> > Thanks!
> >
> > -- A
> >
> >
> > On Thu, Feb 11, 2016 at 3:43 PM, Robert D. Vincent <
> > robert.d.vincent at mcgill.ca> wrote:
> >
> > > Hi Alex,
> > >
> > > That is surprising. There is only one position indicated in the file,
> and
> > > we are correctly reading it as 0, 0, 0 (it's a DICOM element 0020,
> 0032).
> > > So as far as we are concerned we're assigning the correct start values.
> > >
> > > It's possible that dcm2nii is "inventing" position values corresponding
> > to
> > > the centre of the grid - are they something like 150.6? (128/2)*2.353
> > >
> > >     -bert
> > >
> > >
> > > On Thu, Feb 11, 2016 at 3:02 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > > wrote:
> > >
> > > > Hi Bert,
> > > >
> > > > Cool - thanks much! The steps/zspace now look good :-)
> > > >
> > > > However I believe that the starts may still be wrong. When run
> through
> > > > dcm2nii - nii2mnc, the volume ends up with start values that I
> suspect
> > > are
> > > > 'real' (they roughly match the corresponding T1 that I have). With
> this
> > > new
> > > > dcm2mnc, the start values are all 0.
> > > >
> > > > -- A
> > > >
> > > > On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
> > > > robert.d.vincent at mcgill.ca> wrote:
> > > >
> > > > > Hi Alex,
> > > > >
> > > > > I just pushed a fix to Github that should put correct Z axis
> spacing
> > in
> > > > > these sequences.
> > > > >
> > > > >     -bert
> > > > >
> > > > > On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <
> > > gdevenyi at gmail.com
> > > > >
> > > > > wrote:
> > > > >
> > > > > > Just a follwup, the "newer" dicom creator is dcm2niix, may be
> able
> > to
> > > > > find
> > > > > > some useful info here https://github.com/neurolabusc/dcm2niix
> > > > > >
> > > > > > --
> > > > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > > > Research Computing Associate
> > > > > > Computational Brain Anatomy Laboratory
> > > > > > Cerebral Imaging Center
> > > > > > Douglas Mental Health University Institute
> > > > > > McGill University
> > > > > > t: 514.761.6131x4781
> > > > > > e: gdevenyi at gmail.com
> > > > > >
> > > > > > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > > > > > robert.d.vincent at mcgill.ca> wrote:
> > > > > >
> > > > > > > Hi Alex,
> > > > > > >
> > > > > > > We've encountered so little 3D DICOM over the years I'm not
> > > surprised
> > > > > it
> > > > > > > isn't handled well.
> > > > > > >
> > > > > > > Thanks for the dataset. I will look into it and let you know.
> > > > > > >
> > > > > > >     -bert
> > > > > > >
> > > > > > >
> > > > > > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <
> > > > zijdenbos at gmail.com>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > I got some 3D DICOM SPECT data that dcm2mnc issues with -
> > > depending
> > > > > on
> > > > > > > what
> > > > > > > > version of dcm2mnc I use, I get somewhat different results;
> but
> > > in
> > > > > most
> > > > > > > > cases I end up with irregular z-spacing and/or a flipped
> > z-axis.
> > > > The
> > > > > > most
> > > > > > > > recent version I tried was dcm2mnc version 2.01.03 from
> > > > minc-toolkit
> > > > > > > > version 1.0.08.
> > > > > > > >
> > > > > > > > If I run the same thing through dcm2nii followed by nii2mnc
> > > > (ugh!), I
> > > > > > > > actually get a volume that looks like I expected. There
> appears
> > > to
> > > > be
> > > > > > > > coordinate space information in the 3D DICOM that dcm2nii
> seems
> > > to
> > > > be
> > > > > > > able
> > > > > > > > to interpret, but dcm2mnc does not.
> > > > > > > >
> > > > > > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > > > > > >
> > > > > > > > Here is a sample DICOM set:
> > > > > > > > ?
> > > > > > > >  s1_0013006_3006.dcm.gz
> > > > > > > > <
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > > > > > >
> > > > > > > > ?
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > >
> > > > > > > > -- A
> > > > > > > > _______________________________________________
> > > > > > > > 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
> > > > > >
> > > > > _______________________________________________
> > > > > 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
> > >
> > _______________________________________________
> > 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 gdevenyi at gmail.com  Tue Feb 16 12:09:33 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 16 Feb 2016 12:09:33 -0500
Subject: [MINC-users] Problems with volume/slice normalization and labels
Message-ID: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>

Hi minc-users,

I have some labels that via some step in minc-toolkit had an introduction
of volume and/or slice-selective normalization.

This is causing serious issues *sometimes* in some processing.

Can anyone recommend a way to successfully strip away all the normalization
from the file so they are true labels?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From andrew at biospective.com  Tue Feb 16 12:15:45 2016
From: andrew at biospective.com (Andrew Wood)
Date: Tue, 16 Feb 2016 12:15:45 -0500
Subject: [MINC-users] Problems with volume/slice normalization and labels
In-Reply-To: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>
References: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>
Message-ID: <CABApf9HQjNJefj_Y2hYyqpD7e8RNeSCsyt0LTvuTfDuZZLyoZA@mail.gmail.com>

Hi Gabriel,

One way is to filter your label volumes through mincreshape, making sure
the image_range and valid_range are the same:

$ mincreshape in.mnc \
-normalize \
-unsigned -byte \
-image_range 0 255 \
-valid_range 0 255 \
fixed.mnc

- Andrew

On Tue, Feb 16, 2016 at 12:09 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Hi minc-users,
>
> I have some labels that via some step in minc-toolkit had an introduction
> of volume and/or slice-selective normalization.
>
> This is causing serious issues *sometimes* in some processing.
>
> Can anyone recommend a way to successfully strip away all the normalization
> from the file so they are true labels?
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Tue Feb 16 13:20:07 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 16 Feb 2016 13:20:07 -0500
Subject: [MINC-users] Problems with volume/slice normalization and labels
In-Reply-To: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>
References: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>
Message-ID: <56C36857.8030605@gmail.com>

itk_resample --labels <in> <out>  --like <template> --transform 
<transform.xfm>  for resampling

or, after running any standard minc tool (minccalc, mincmath, etc )

mincreshape -valid_range 0 X -image_range 0 X <in> <out>

where X in you maximum label id

On 16-02-16 12:09 PM, Gabriel A. Devenyi wrote:
> Hi minc-users,
>
> I have some labels that via some step in minc-toolkit had an introduction
> of volume and/or slice-selective normalization.
>
> This is causing serious issues *sometimes* in some processing.
>
> Can anyone recommend a way to successfully strip away all the normalization
> from the file so they are true labels?
>


-- 
Best regards,

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

From gdevenyi at gmail.com  Sat Feb 20 16:36:34 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Sat, 20 Feb 2016 16:36:34 -0500
Subject: [MINC-users] Problems with volume/slice normalization and labels
In-Reply-To: <56C36857.8030605@gmail.com>
References: <CAFQOoOqV9LgAhp8azcBfF+D+AiGv6zzqpRPB+v1S_ndVek_qLw@mail.gmail.com>
	<56C36857.8030605@gmail.com>
Message-ID: <CAFQOoOqiZ0CKL62PzZEskfB-89k7c8z64rDBOhB7ZG_aeOij9A@mail.gmail.com>

Thanks Vlad, we've moved to itk_resample for our transforms previously on
your recommendation.



-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Tue, Feb 16, 2016 at 1:20 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> itk_resample --labels <in> <out>  --like <template> --transform
> <transform.xfm>  for resampling
>
> or, after running any standard minc tool (minccalc, mincmath, etc )
>
> mincreshape -valid_range 0 X -image_range 0 X <in> <out>
>
> where X in you maximum label id
>
> On 16-02-16 12:09 PM, Gabriel A. Devenyi wrote:
>
>> Hi minc-users,
>>
>> I have some labels that via some step in minc-toolkit had an introduction
>> of volume and/or slice-selective normalization.
>>
>> This is causing serious issues *sometimes* in some processing.
>>
>> Can anyone recommend a way to successfully strip away all the
>> normalization
>> from the file so they are true labels?
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From louis.dieumegarde at crulrg.ulaval.ca  Wed Feb 24 10:58:24 2016
From: louis.dieumegarde at crulrg.ulaval.ca (Louis Dieumegarde)
Date: Wed, 24 Feb 2016 15:58:24 +0000
Subject: [MINC-users] itk_resample vs mincresample
Message-ID: <27869E2D-F01F-4E27-B658-8E153B16ECE5@ulaval.ca>

Bonjour,

We had problems with the labels values being re-evaluate with mincresample when we do a nereast-neighbour.

I?m trying itk_resample as suggested with the ?labels option but it seems to do the same.

Is the option ?normalize of itk_resample should be consider as it seems to keep the exact value of labels?
What is the difference between ?normalize and ?labels options?

Merci. 

Louis Dieumegarde, B.Sc.
Professionnel de recherche
Laboratoire Medics, local F-3568
Centre de Recherche de l?Institut Universitaire en Sant? Mentale de Qu?bec
2601 Chemin de la Canardi?re, Qu?bec
G1J 2G3, Canada
(418) 663-5000, poste 6716
louis.dieumegarde at crulrg.ulaval.ca









On 2016-02-21, 12:00 PM, "minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca" <minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca> wrote:

>Send MINC-users mailing list submissions to
>	minc-users at bic.mni.mcgill.ca
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>or, via email, send a message with subject or body 'help' to
>	minc-users-request at bic.mni.mcgill.ca
>
>You can reach the person managing the list at
>	minc-users-owner at bic.mni.mcgill.ca
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of MINC-users digest..."
>
>
>Today's Topics:
>
>   1. Re: Problems with volume/slice normalization and labels
>      (Gabriel A. Devenyi)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Sat, 20 Feb 2016 16:36:34 -0500
>From: "Gabriel A. Devenyi" <gdevenyi at gmail.com>
>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>Subject: Re: [MINC-users] Problems with volume/slice normalization and
>	labels
>Message-ID:
>	<CAFQOoOqiZ0CKL62PzZEskfB-89k7c8z64rDBOhB7ZG_aeOij9A at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Thanks Vlad, we've moved to itk_resample for our transforms previously on
>your recommendation.
>
>
>
>-- 
>Gabriel A. Devenyi B.Eng. Ph.D.
>Research Computing Associate
>Computational Brain Anatomy Laboratory
>Cerebral Imaging Center
>Douglas Mental Health University Institute
>McGill University
>t: 514.761.6131x4781
>e: gdevenyi at gmail.com
>
>On Tue, Feb 16, 2016 at 1:20 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>> wrote:
>
>> itk_resample --labels <in> <out>  --like <template> --transform
>> <transform.xfm>  for resampling
>>
>> or, after running any standard minc tool (minccalc, mincmath, etc )
>>
>> mincreshape -valid_range 0 X -image_range 0 X <in> <out>
>>
>> where X in you maximum label id
>>
>> On 16-02-16 12:09 PM, Gabriel A. Devenyi wrote:
>>
>>> Hi minc-users,
>>>
>>> I have some labels that via some step in minc-toolkit had an introduction
>>> of volume and/or slice-selective normalization.
>>>
>>> This is causing serious issues *sometimes* in some processing.
>>>
>>> Can anyone recommend a way to successfully strip away all the
>>> normalization
>>> from the file so they are true labels?
>>>
>>>
>>
>> --
>> Best regards,
>>
>>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>------------------------------
>
>_______________________________________________
>MINC-users mailing list
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
>End of MINC-users Digest, Vol 126, Issue 11
>*******************************************

From vladimir.fonov at gmail.com  Wed Feb 24 11:33:23 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 24 Feb 2016 11:33:23 -0500
Subject: [MINC-users] itk_resample vs mincresample
In-Reply-To: <27869E2D-F01F-4E27-B658-8E153B16ECE5@ulaval.ca>
References: <27869E2D-F01F-4E27-B658-8E153B16ECE5@ulaval.ca>
Message-ID: <56CDDB53.6040408@gmail.com>

Hello,


are you sure that your input file doesn't have this problem?
What is the output of
mincheader volume.mnc |grep 'image-min\|image-max'


--normalize switch has nothing to do with interpolation of labels, it 
only affects spacial sampling.

On 16-02-24 10:58 AM, Louis Dieumegarde wrote:
> Bonjour,
>
> We had problems with the labels values being re-evaluate with mincresample when we do a nereast-neighbour.
>
> I?m trying itk_resample as suggested with the ?labels option but it seems to do the same.
>
> Is the option ?normalize of itk_resample should be consider as it seems to keep the exact value of labels?
> What is the difference between ?normalize and ?labels options?
>
> Merci.
>
> Louis Dieumegarde, B.Sc.
> Professionnel de recherche
> Laboratoire Medics, local F-3568
> Centre de Recherche de l?Institut Universitaire en Sant? Mentale de Qu?bec
> 2601 Chemin de la Canardi?re, Qu?bec
> G1J 2G3, Canada
> (418) 663-5000, poste 6716
> louis.dieumegarde at crulrg.ulaval.ca
>
>
>
>
>
>
>
>
>
> On 2016-02-21, 12:00 PM, "minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca" <minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca> wrote:
>
>> Send MINC-users mailing list submissions to
>> 	minc-users at bic.mni.mcgill.ca
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> or, via email, send a message with subject or body 'help' to
>> 	minc-users-request at bic.mni.mcgill.ca
>>
>> You can reach the person managing the list at
>> 	minc-users-owner at bic.mni.mcgill.ca
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of MINC-users digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Re: Problems with volume/slice normalization and labels
>>       (Gabriel A. Devenyi)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 20 Feb 2016 16:36:34 -0500
>> From: "Gabriel A. Devenyi" <gdevenyi at gmail.com>
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Subject: Re: [MINC-users] Problems with volume/slice normalization and
>> 	labels
>> Message-ID:
>> 	<CAFQOoOqiZ0CKL62PzZEskfB-89k7c8z64rDBOhB7ZG_aeOij9A at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thanks Vlad, we've moved to itk_resample for our transforms previously on
>> your recommendation.
>>
>>
>>
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>>
>> On Tue, Feb 16, 2016 at 1:20 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>>> wrote:
>>
>>> itk_resample --labels <in> <out>  --like <template> --transform
>>> <transform.xfm>  for resampling
>>>
>>> or, after running any standard minc tool (minccalc, mincmath, etc )
>>>
>>> mincreshape -valid_range 0 X -image_range 0 X <in> <out>
>>>
>>> where X in you maximum label id
>>>
>>> On 16-02-16 12:09 PM, Gabriel A. Devenyi wrote:
>>>
>>>> Hi minc-users,
>>>>
>>>> I have some labels that via some step in minc-toolkit had an introduction
>>>> of volume and/or slice-selective normalization.
>>>>
>>>> This is causing serious issues *sometimes* in some processing.
>>>>
>>>> Can anyone recommend a way to successfully strip away all the
>>>> normalization
>>>> from the file so they are true labels?
>>>>
>>>>
>>>
>>> --
>>> Best regards,
>>>
>>>   Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> MINC-users mailing list
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
>> End of MINC-users Digest, Vol 126, Issue 11
>> *******************************************
> _______________________________________________
> 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 gdevenyi at gmail.com  Fri Feb 26 11:37:38 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Fri, 26 Feb 2016 11:37:38 -0500
Subject: [MINC-users] The story of "bestlinreg"?
Message-ID: <CAFQOoOrBZaeC5RkGMDK13cSJHoERG+bnC9U0AUsO20oKAWA9UQ@mail.gmail.com>

Hi minc-users,

I was wondering if anyone had any background about the various versions of
bestlinreg around.
So far I've seen
bestlinreg
bestlinreg.pl
bestlinreg_s
bestlinreg_s2

I've looked over the help and diffed the various versions together and I
see some differences, but its not clear to me why so many exist or if
they're intended for different purposes.

Does anyone have the story of their pedigree?

Thanks!

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From claude at bic.mni.mcgill.ca  Fri Feb 26 12:22:42 2016
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 26 Feb 2016 12:22:42 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <CAFQOoOrBZaeC5RkGMDK13cSJHoERG+bnC9U0AUsO20oKAWA9UQ@mail.gmail.com>
Message-ID: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>

Hi,

A few historical notes here...

Oliver and I are at the origin of the creation of bestlinreg.pl.
The motivation was to split the original mritotal script into a
module for linear registration and one for non-linear registration.
Being modest, we, of course, called it "best". bestlinreg.pl typically
lives within the CIVET pipeline and hasn't be formally added to 
the mni autoreg package. bestlinreg.pl has thus evolved with the
versions of CIVET over the years, although we have not renamed it
bestbestlinreg.pl.

I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
from. Likely, they are other flavours of bestlinreg.pl. 

Claude


>
> Hi minc-users,
>
> I was wondering if anyone had any background about the various versions of
> bestlinreg around.
> So far I've seen
> bestlinreg
> bestlinreg.pl
> bestlinreg_s
> bestlinreg_s2
>
> I've looked over the help and diffed the various versions together and I
> see some differences, but its not clear to me why so many exist or if
> they're intended for different purposes.
>
> Does anyone have the story of their pedigree?
>
> Thanks!
>
> -- 
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com

From vladimir.fonov at gmail.com  Fri Feb 26 12:32:05 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 26 Feb 2016 12:32:05 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
References: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
Message-ID: <56D08C15.1060902@gmail.com>

Hello,

bestlinreg_s and _s2 are my alternations of the original script.

All three are part of minc_toolkit , see 
https://github.com/BIC-MNI/EZminc/tree/master/scripts


On 16-02-26 12:22 PM, Claude LEPAGE wrote:
> Hi,
>
> A few historical notes here...
>
> Oliver and I are at the origin of the creation of bestlinreg.pl.
> The motivation was to split the original mritotal script into a
> module for linear registration and one for non-linear registration.
> Being modest, we, of course, called it "best". bestlinreg.pl typically
> lives within the CIVET pipeline and hasn't be formally added to
> the mni autoreg package. bestlinreg.pl has thus evolved with the
> versions of CIVET over the years, although we have not renamed it
> bestbestlinreg.pl.
>
> I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
> from. Likely, they are other flavours of bestlinreg.pl.
>
> Claude
>
>
>>
>> Hi minc-users,
>>
>> I was wondering if anyone had any background about the various versions of
>> bestlinreg around.
>> So far I've seen
>> bestlinreg
>> bestlinreg.pl
>> bestlinreg_s
>> bestlinreg_s2
>>
>> I've looked over the help and diffed the various versions together and I
>> see some differences, but its not clear to me why so many exist or if
>> they're intended for different purposes.
>>
>> Does anyone have the story of their pedigree?
>>
>> Thanks!
>>
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
> _______________________________________________
> 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 zijdenbos at gmail.com  Fri Feb 26 13:07:59 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 26 Feb 2016 13:07:59 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <56D08C15.1060902@gmail.com>
References: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
	<56D08C15.1060902@gmail.com>
Message-ID: <CABEEk16PRT1uPjmW==WeY67_Q=+c0XJa=mGJDsComLehZUt-CA@mail.gmail.com>

I always thought the 's' referred to Steve Robbins, who did some parameter
optimization on these registration protocol (bestlinreg_s and nlfit_s)?
That not correct then?

On Fri, Feb 26, 2016 at 12:32 PM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> Hello,
>
> bestlinreg_s and _s2 are my alternations of the original script.
>
> All three are part of minc_toolkit , see
> https://github.com/BIC-MNI/EZminc/tree/master/scripts
>
>
>
> On 16-02-26 12:22 PM, Claude LEPAGE wrote:
>
>> Hi,
>>
>> A few historical notes here...
>>
>> Oliver and I are at the origin of the creation of bestlinreg.pl.
>> The motivation was to split the original mritotal script into a
>> module for linear registration and one for non-linear registration.
>> Being modest, we, of course, called it "best". bestlinreg.pl typically
>> lives within the CIVET pipeline and hasn't be formally added to
>> the mni autoreg package. bestlinreg.pl has thus evolved with the
>> versions of CIVET over the years, although we have not renamed it
>> bestbestlinreg.pl.
>>
>> I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
>> from. Likely, they are other flavours of bestlinreg.pl.
>>
>> Claude
>>
>>
>>
>>> Hi minc-users,
>>>
>>> I was wondering if anyone had any background about the various versions
>>> of
>>> bestlinreg around.
>>> So far I've seen
>>> bestlinreg
>>> bestlinreg.pl
>>> bestlinreg_s
>>> bestlinreg_s2
>>>
>>> I've looked over the help and diffed the various versions together and I
>>> see some differences, but its not clear to me why so many exist or if
>>> they're intended for different purposes.
>>>
>>> Does anyone have the story of their pedigree?
>>>
>>> Thanks!
>>>
>>> --
>>> Gabriel A. Devenyi B.Eng. Ph.D.
>>> Research Computing Associate
>>> Computational Brain Anatomy Laboratory
>>> Cerebral Imaging Center
>>> Douglas Mental Health University Institute
>>> McGill University
>>> t: 514.761.6131x4781
>>> e: gdevenyi at gmail.com
>>>
>> _______________________________________________
>> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From vladimir.fonov at gmail.com  Fri Feb 26 13:31:10 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 26 Feb 2016 13:31:10 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <CABEEk16PRT1uPjmW==WeY67_Q=+c0XJa=mGJDsComLehZUt-CA@mail.gmail.com>
References: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
	<56D08C15.1060902@gmail.com>
	<CABEEk16PRT1uPjmW==WeY67_Q=+c0XJa=mGJDsComLehZUt-CA@mail.gmail.com>
Message-ID: <56D099EE.4030809@gmail.com>

No, both are mine.

On 16-02-26 01:07 PM, Alex Zijdenbos wrote:
> I always thought the 's' referred to Steve Robbins, who did some parameter
> optimization on these registration protocol (bestlinreg_s and nlfit_s)?
> That not correct then?
>
> On Fri, Feb 26, 2016 at 12:32 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com> wrote:
>
>> Hello,
>>
>> bestlinreg_s and _s2 are my alternations of the original script.
>>
>> All three are part of minc_toolkit , see
>> https://github.com/BIC-MNI/EZminc/tree/master/scripts
>>
>>
>>
>> On 16-02-26 12:22 PM, Claude LEPAGE wrote:
>>
>>> Hi,
>>>
>>> A few historical notes here...
>>>
>>> Oliver and I are at the origin of the creation of bestlinreg.pl.
>>> The motivation was to split the original mritotal script into a
>>> module for linear registration and one for non-linear registration.
>>> Being modest, we, of course, called it "best". bestlinreg.pl typically
>>> lives within the CIVET pipeline and hasn't be formally added to
>>> the mni autoreg package. bestlinreg.pl has thus evolved with the
>>> versions of CIVET over the years, although we have not renamed it
>>> bestbestlinreg.pl.
>>>
>>> I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
>>> from. Likely, they are other flavours of bestlinreg.pl.
>>>
>>> Claude
>>>
>>>
>>>
>>>> Hi minc-users,
>>>>
>>>> I was wondering if anyone had any background about the various versions
>>>> of
>>>> bestlinreg around.
>>>> So far I've seen
>>>> bestlinreg
>>>> bestlinreg.pl
>>>> bestlinreg_s
>>>> bestlinreg_s2
>>>>
>>>> I've looked over the help and diffed the various versions together and I
>>>> see some differences, but its not clear to me why so many exist or if
>>>> they're intended for different purposes.
>>>>
>>>> Does anyone have the story of their pedigree?
>>>>
>>>> Thanks!
>>>>
>>>> --
>>>> Gabriel A. Devenyi B.Eng. Ph.D.
>>>> Research Computing Associate
>>>> Computational Brain Anatomy Laboratory
>>>> Cerebral Imaging Center
>>>> Douglas Mental Health University Institute
>>>> McGill University
>>>> t: 514.761.6131x4781
>>>> e: gdevenyi at gmail.com
>>>>
>>> _______________________________________________
>>> 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
>> _______________________________________________
>> 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.fonov <at> gmail.com

From zijdenbos at gmail.com  Fri Feb 26 13:46:37 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 26 Feb 2016 13:46:37 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <56D099EE.4030809@gmail.com>
References: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
	<56D08C15.1060902@gmail.com>
	<CABEEk16PRT1uPjmW==WeY67_Q=+c0XJa=mGJDsComLehZUt-CA@mail.gmail.com>
	<56D099EE.4030809@gmail.com>
Message-ID: <CABEEk17p60g=mD8viPL-Jjs0hXC+Qxy94Z49SEPQxiccUevFdg@mail.gmail.com>

I stand corrected then. Vladimir 'S' Fonov :)

On Fri, Feb 26, 2016 at 1:31 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> No, both are mine.
>
>
> On 16-02-26 01:07 PM, Alex Zijdenbos wrote:
>
>> I always thought the 's' referred to Steve Robbins, who did some parameter
>> optimization on these registration protocol (bestlinreg_s and nlfit_s)?
>> That not correct then?
>>
>> On Fri, Feb 26, 2016 at 12:32 PM, Vladimir S. FONOV <
>> vladimir.fonov at gmail.com> wrote:
>>
>> Hello,
>>>
>>> bestlinreg_s and _s2 are my alternations of the original script.
>>>
>>> All three are part of minc_toolkit , see
>>> https://github.com/BIC-MNI/EZminc/tree/master/scripts
>>>
>>>
>>>
>>> On 16-02-26 12:22 PM, Claude LEPAGE wrote:
>>>
>>> Hi,
>>>>
>>>> A few historical notes here...
>>>>
>>>> Oliver and I are at the origin of the creation of bestlinreg.pl.
>>>> The motivation was to split the original mritotal script into a
>>>> module for linear registration and one for non-linear registration.
>>>> Being modest, we, of course, called it "best". bestlinreg.pl typically
>>>> lives within the CIVET pipeline and hasn't be formally added to
>>>> the mni autoreg package. bestlinreg.pl has thus evolved with the
>>>> versions of CIVET over the years, although we have not renamed it
>>>> bestbestlinreg.pl.
>>>>
>>>> I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
>>>> from. Likely, they are other flavours of bestlinreg.pl.
>>>>
>>>> Claude
>>>>
>>>>
>>>>
>>>> Hi minc-users,
>>>>>
>>>>> I was wondering if anyone had any background about the various versions
>>>>> of
>>>>> bestlinreg around.
>>>>> So far I've seen
>>>>> bestlinreg
>>>>> bestlinreg.pl
>>>>> bestlinreg_s
>>>>> bestlinreg_s2
>>>>>
>>>>> I've looked over the help and diffed the various versions together and
>>>>> I
>>>>> see some differences, but its not clear to me why so many exist or if
>>>>> they're intended for different purposes.
>>>>>
>>>>> Does anyone have the story of their pedigree?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> --
>>>>> Gabriel A. Devenyi B.Eng. Ph.D.
>>>>> Research Computing Associate
>>>>> Computational Brain Anatomy Laboratory
>>>>> Cerebral Imaging Center
>>>>> Douglas Mental Health University Institute
>>>>> McGill University
>>>>> t: 514.761.6131x4781
>>>>> e: gdevenyi at gmail.com
>>>>>
>>>>> _______________________________________________
>>>> 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
>>> _______________________________________________
>>> 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.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From vladimir.fonov at gmail.com  Fri Feb 26 13:53:29 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 26 Feb 2016 13:53:29 -0500
Subject: [MINC-users] The story of "bestlinreg"?
In-Reply-To: <CABEEk17p60g=mD8viPL-Jjs0hXC+Qxy94Z49SEPQxiccUevFdg@mail.gmail.com>
References: <201602261722.u1QHMgZ3019135@login1.bic.mni.mcgill.ca>
	<56D08C15.1060902@gmail.com>
	<CABEEk16PRT1uPjmW==WeY67_Q=+c0XJa=mGJDsComLehZUt-CA@mail.gmail.com>
	<56D099EE.4030809@gmail.com>
	<CABEEk17p60g=mD8viPL-Jjs0hXC+Qxy94Z49SEPQxiccUevFdg@mail.gmail.com>
Message-ID: <56D09F29.1090900@gmail.com>

no, the real reason is now forgotten. But I also happen to have nlfit_l


On 16-02-26 01:46 PM, Alex Zijdenbos wrote:
> I stand corrected then. Vladimir 'S' Fonov :)
>
> On Fri, Feb 26, 2016 at 1:31 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>> wrote:
>
>> No, both are mine.
>>
>>
>> On 16-02-26 01:07 PM, Alex Zijdenbos wrote:
>>
>>> I always thought the 's' referred to Steve Robbins, who did some parameter
>>> optimization on these registration protocol (bestlinreg_s and nlfit_s)?
>>> That not correct then?
>>>
>>> On Fri, Feb 26, 2016 at 12:32 PM, Vladimir S. FONOV <
>>> vladimir.fonov at gmail.com> wrote:
>>>
>>> Hello,
>>>>
>>>> bestlinreg_s and _s2 are my alternations of the original script.
>>>>
>>>> All three are part of minc_toolkit , see
>>>> https://github.com/BIC-MNI/EZminc/tree/master/scripts
>>>>
>>>>
>>>>
>>>> On 16-02-26 12:22 PM, Claude LEPAGE wrote:
>>>>
>>>> Hi,
>>>>>
>>>>> A few historical notes here...
>>>>>
>>>>> Oliver and I are at the origin of the creation of bestlinreg.pl.
>>>>> The motivation was to split the original mritotal script into a
>>>>> module for linear registration and one for non-linear registration.
>>>>> Being modest, we, of course, called it "best". bestlinreg.pl typically
>>>>> lives within the CIVET pipeline and hasn't be formally added to
>>>>> the mni autoreg package. bestlinreg.pl has thus evolved with the
>>>>> versions of CIVET over the years, although we have not renamed it
>>>>> bestbestlinreg.pl.
>>>>>
>>>>> I don't know where bestlinreg, bestlinreg_s, and bestlinreg_s2 are
>>>>> from. Likely, they are other flavours of bestlinreg.pl.
>>>>>
>>>>> Claude
>>>>>
>>>>>
>>>>>
>>>>> Hi minc-users,
>>>>>>
>>>>>> I was wondering if anyone had any background about the various versions
>>>>>> of
>>>>>> bestlinreg around.
>>>>>> So far I've seen
>>>>>> bestlinreg
>>>>>> bestlinreg.pl
>>>>>> bestlinreg_s
>>>>>> bestlinreg_s2
>>>>>>
>>>>>> I've looked over the help and diffed the various versions together and
>>>>>> I
>>>>>> see some differences, but its not clear to me why so many exist or if
>>>>>> they're intended for different purposes.
>>>>>>
>>>>>> Does anyone have the story of their pedigree?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> --
>>>>>> Gabriel A. Devenyi B.Eng. Ph.D.
>>>>>> Research Computing Associate
>>>>>> Computational Brain Anatomy Laboratory
>>>>>> Cerebral Imaging Center
>>>>>> Douglas Mental Health University Institute
>>>>>> McGill University
>>>>>> t: 514.761.6131x4781
>>>>>> e: gdevenyi at gmail.com
>>>>>>
>>>>>> _______________________________________________
>>>>> 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
>>>> _______________________________________________
>>>> 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.fonov <at> gmail.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.fonov <at> gmail.com

From andrew at biospective.com  Fri Feb 26 14:36:21 2016
From: andrew at biospective.com (Andrew Wood)
Date: Fri, 26 Feb 2016 14:36:21 -0500
Subject: [MINC-users] mincdiff on world values
Message-ID: <CABApf9FZVZnPQsO1dhFC0LGWYKpVNXmGCJtqZEMeHccWp4j0KQ@mail.gmail.com>

Hi all,

I came across some interesting behavior with mincdiff:

$ make_phantom ./phantom.mnc
$ mincmath -add -const 1 ./phantom.mnc ./phantom2.mnc
$ mincdiff phantom.mnc phantom2.mnc
...
>     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
>     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ;
67c75,80
<  image-max = 1 ;
---
>  image-max = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
>     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
>     1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2,
>     2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
>     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
>     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ;
Binary image comparison:
Images are identical.


mincmath didn't change the image block, but rather modified the header to
change how the voxel values are interpreted, so mincdiff's body comparison
reported equality.

>From a user perspective, it doesn't feel right to see "Images are
identical" for images that a clearly different. I suppose mincdiff is doing
what it advertises, but it might be confusing for some users. I was
wondering if it'd make sense to make mincdiff (optionally) compare *real*
values, since users are typically more interested in those than they are
*voxel* values.

Cheers,
Andrew

From robert.d.vincent at mcgill.ca  Fri Feb 26 14:45:10 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Fri, 26 Feb 2016 14:45:10 -0500
Subject: [MINC-users] mincdiff on world values
In-Reply-To: <CABApf9FZVZnPQsO1dhFC0LGWYKpVNXmGCJtqZEMeHccWp4j0KQ@mail.gmail.com>
References: <CABApf9FZVZnPQsO1dhFC0LGWYKpVNXmGCJtqZEMeHccWp4j0KQ@mail.gmail.com>
Message-ID: <CAAd5DeQrZf2qyUggYM1QnUHG7+PP6WZTtezs4-cggfGaE=svUQ@mail.gmail.com>

Hi Andrew,

Interesting point. Mincdiff is really mostly a tool for comparing headers.
If you want to compare voxel values, minccmp is much more appropriate.

I agree that it might be good to give a slightly more useful message in
mincdiff.

    -bert
On Feb 26, 2016 2:37 PM, "Andrew Wood" <andrew at biospective.com> wrote:

> Hi all,
>
> I came across some interesting behavior with mincdiff:
>
> $ make_phantom ./phantom.mnc
> $ mincmath -add -const 1 ./phantom.mnc ./phantom2.mnc
> $ mincdiff phantom.mnc phantom2.mnc
> ...
> >     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1,
> >     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ;
> 67c75,80
> <  image-max = 1 ;
> ---
> >  image-max = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1,
> >     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1,
> >     1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2,
> >     2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1,
> >     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1,
> >     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ;
> Binary image comparison:
> Images are identical.
>
>
> mincmath didn't change the image block, but rather modified the header to
> change how the voxel values are interpreted, so mincdiff's body comparison
> reported equality.
>
> From a user perspective, it doesn't feel right to see "Images are
> identical" for images that a clearly different. I suppose mincdiff is doing
> what it advertises, but it might be confusing for some users. I was
> wondering if it'd make sense to make mincdiff (optionally) compare *real*
> values, since users are typically more interested in those than they are
> *voxel* values.
>
> Cheers,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>