From danielkim at gist.ac.kr  Sat Mar  2 02:10:17 2013
From: danielkim at gist.ac.kr (Donghyeon Kim)
Date: Sat, 2 Mar 2013 16:10:17 +0900 (KST)
Subject: [MINC-users] Display and register problem.
Message-ID: <1497123768.1362208217561.JavaMail.root@eunhasu>

Hi all,



I tried to install MINC tool-kit on my computer. When i installed MINC-toolkit, however, register and Display works improperly on virtual machine and native os (Ubuntu 12.10 x64).

When I run Display, only Display:Menu is appeared, 3D view doesn't be appered. When I run register, sometimes image is just black. Maybe problem is graphic card driver.

Does anyone have a same problem? how can I solve this problem?






 

    
        
            -------------------------------------------------- 

            DONGHYEON KIM, PhD Student 

            Dept. of Info. &amp; Comm., Gwangju Institute of Science and Technology(GIST) 

            261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea

            Tel: +82-62-715-2266 Cell: +82-10-9361-3781

            E-mail: danielkim at gist.ac.kr URL: https://biocomput.gist.ac.kr

             
        
    



From a.janke at gmail.com  Sun Mar  3 08:40:37 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 3 Mar 2013 23:40:37 +1000
Subject: [MINC-users] Display and register problem.
In-Reply-To: <1497123768.1362208217561.JavaMail.root@eunhasu>
References: <1497123768.1362208217561.JavaMail.root@eunhasu>
Message-ID: <CAG0CB22NkYDj2xzEfF86YRJs1PWqOooC_amfYEPVnbm8fTUW8w@mail.gmail.com>

Hi,

On 2 March 2013 17:10, Donghyeon Kim <danielkim at gist.ac.kr> wrote:
> I tried to install MINC tool-kit on my computer. When i installed MINC-toolkit, however, register and Display works improperly on virtual machine and native os (Ubuntu 12.10 x64).
>
> When I run Display, only Display:Menu is appeared, 3D view doesn't be appered. When I run register, sometimes image is just black. Maybe problem is graphic card driver.
>
> Does anyone have a same problem? how can I solve this problem?

I am certain that this is a GLUT/freeglut problem and thus could be a
video card issue. In the later versions of GLUT that come with Ubuntu
I have seen this, I haven't yet found a solution that works in all
cases.

So, if you are using HW graphics acceleration in the VM, I'd recommend
trying emulation and if not vice versa!

I am keen to find a comprehensive fix for this but don't have enough
consistent error reports on it yet.

Thanks


a

From vladimir.fonov at gmail.com  Sun Mar  3 10:50:42 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Sun, 3 Mar 2013 10:50:42 -0500
Subject: [MINC-users] Display and register problem.
In-Reply-To: <1497123768.1362208217561.JavaMail.root@eunhasu>
References: <1497123768.1362208217561.JavaMail.root@eunhasu>
Message-ID: <E37CE6F5-6F18-45E0-AA14-199DF3FC944B@gmail.com>

Hello Donghyeon,


try setting environment variable LIBGL_ALWAYS_INDIRECT to 1 before running Display or register


i.e 

> export LIBGL_ALWAYS_INDIRECT=1
> register some_file.mnc 


On 2013-03-02, at 2:10 AM, Donghyeon Kim <danielkim at gist.ac.kr> wrote:

> I tried to install MINC tool-kit on my computer. When i installed MINC-toolkit, however, register and Display works improperly on virtual machine and native os (Ubuntu 12.10 x64).
> 
> When I run Display, only Display:Menu is appeared, 3D view doesn't be appered. When I run register, sometimes image is just black. Maybe problem is graphic card driver.
> 
> Does anyone have a same problem? how can I solve this problem?

---
Best regards,

Vladimir S. FONOV 






From danielkim at gist.ac.kr  Wed Mar  6 08:20:48 2013
From: danielkim at gist.ac.kr (Donghyeon Kim)
Date: Wed, 6 Mar 2013 22:20:48 +0900 (KST)
Subject: [MINC-users] Display and register problem.
In-Reply-To: <E37CE6F5-6F18-45E0-AA14-199DF3FC944B@gmail.com>
Message-ID: <348826915.1362576048670.JavaMail.root@eunhasu>

Hi Vladimir,



When I LIBGL_ALWAYS_INDIRECT=1 and run Display with some surface file(*.obj), It doesn't occur error, but I cannot see surface image. 

I think that if Display cannot show 3D view, i may contain error, how can I see error log?

(register is ok, if I didn't choose wrong image (i.e image intensity is very low (10^10)))



Donghyeon

--- Original Message ---

>From    :  "Vladimir S. FONOV"<vladimir.fonov at gmail.com>

To      :  "Donghyeon Kim"<danielkim at gist.ac.kr>, "MINC users mailing list"<minc-users at bic.mni.mcgill.ca>

Date    :  2013/03/04 ??? ?? 12:50:42

Subject :  register some_file.mnc  





On 2013-03-02, at 2:10 AM, Donghyeon Kim <danielkim at gist.ac.kr> Does anyone have a same problem? how can I solve this problem? 



--- 

Best regards, 



Vladimir S. FONOV






 

    
        
            -------------------------------------------------- 

            DONGHYEON KIM, PhD Student 

            Dept. of Info. &amp; Comm., Gwangju Institute of Science and Technology(GIST) 

            261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea

            Tel: +82-62-715-2266 Cell: +82-10-9361-3781

            E-mail: danielkim at gist.ac.kr URL: https://biocomput.gist.ac.kr

             
        
    



From assemlal at cim.mcgill.ca  Thu Mar  7 09:42:26 2013
From: assemlal at cim.mcgill.ca (Haz-Edine Assemlal)
Date: Thu, 7 Mar 2013 09:42:26 -0500
Subject: [MINC-users] Display and register problem.
In-Reply-To: <348826915.1362576048670.JavaMail.root@eunhasu>
References: <348826915.1362576048670.JavaMail.root@eunhasu>
Message-ID: <0948948A-7032-4A7F-8473-0F5CBBDAE284@cim.mcgill.ca>

Hi Donghyeon,

You may try running display with:
Display -global Hide_3D_window FALSE -global Hide_menu_window FALSE

If it fixes the problem, you can add these parameters to your ~/Display.globals
Let me know.

Best,
Haz-Edine

On 2013-03-06, at 8:20 AM, Donghyeon Kim <danielkim at gist.ac.kr> wrote:

> Hi Vladimir,
> 
> 
> 
> When I LIBGL_ALWAYS_INDIRECT=1 and run Display with some surface file(*.obj), It doesn't occur error, but I cannot see surface image. 
> 
> I think that if Display cannot show 3D view, i may contain error, how can I see error log?
> 
> (register is ok, if I didn't choose wrong image (i.e image intensity is very low (10^10)))
> 
> 
> 
> Donghyeon
> 
> --- Original Message ---
> 
> From    :  "Vladimir S. FONOV"<vladimir.fonov at gmail.com>
> 
> To      :  "Donghyeon Kim"<danielkim at gist.ac.kr>, "MINC users mailing list"<minc-users at bic.mni.mcgill.ca>
> 
> Date    :  2013/03/04 ??? ?? 12:50:42
> 
> Subject :  register some_file.mnc  
> 
> 
> 
> 
> 
> On 2013-03-02, at 2:10 AM, Donghyeon Kim <danielkim at gist.ac.kr> Does anyone have a same problem? how can I solve this problem? 
> 
> 
> 
> --- 
> 
> Best regards, 
> 
> 
> 
> Vladimir S. FONOV
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>            -------------------------------------------------- 
> 
>            DONGHYEON KIM, PhD Student 
> 
>            Dept. of Info. &amp; Comm., Gwangju Institute of Science and Technology(GIST) 
> 
>            261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea
> 
>            Tel: +82-62-715-2266 Cell: +82-10-9361-3781
> 
>            E-mail: danielkim at gist.ac.kr URL: https://biocomput.gist.ac.kr
> 
> 
> 
> 
> 
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From eskild at gmail.com  Thu Mar  7 11:15:57 2013
From: eskild at gmail.com (Simon Eskildsen)
Date: Thu, 7 Mar 2013 17:15:57 +0100
Subject: [MINC-users] mincbeast 1.15 released
Message-ID: <CAD3v436URGvf3euzq7saME6boq4UrKrHKOABdPJGsSePJbn=_Q@mail.gmail.com>

Hi all,

A new version of mincbeast is now available through the BIC website:

http://www.bic.mni.mcgill.ca/ServicesSoftwareAdvancedImageProcessingTools/BEaST/

mincbeast is a MINC implementation of BEaST - a patch based brain
extraction algorithm (for T1w MRI).

A precompiled binary for Linux x86_64 systems is available along with the
source code. The bleeding edge source can always be found at:

https://github.com/BIC-MNI/BEaST

The latest version (1.15) has documentation on how to build a template
library of ICBM and ADNI data as well has how to tailor a library specific
studies. Further information is provided here:

https://github.com/BIC-MNI/BEaST/blob/master/README
https://github.com/BIC-MNI/BEaST/blob/master/README.library

Have a great day.
Simon

From zijdenbos at gmail.com  Mon Mar 18 00:07:08 2013
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 18 Mar 2013 00:07:08 -0400
Subject: [MINC-users] Of clobbering
Message-ID: <CABEEk167_xAo6qD7tz=+mH2v5rKXjxkLYp4m4LQNgRCWGfUjMA@mail.gmail.com>

Hi all,

I just realized that when clobbering an output file that is a symbolic
link, several (all?) minc tools will (try to) clobber the target of the
link instead of the link itself.

For example:

$ ln -s target.mnc symlink.mnc
$ mincmath -clobber -gt -const 0 <in.mnc> symlink.mnc

will overwrite target.mnc instead of symlink.mnc.

I tested this with a few tools (mincaverage, mincmath, mincmorph, minccalc,
mincresample) and all of them behave this way.

IMHO this is actually _really_ bad behaviour; so I was wondering what
others thought of this, and if this was done by design?

-- Alex

From a.janke at gmail.com  Mon Mar 18 00:31:16 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 18 Mar 2013 14:31:16 +1000
Subject: [MINC-users] Of clobbering
In-Reply-To: <CABEEk167_xAo6qD7tz=+mH2v5rKXjxkLYp4m4LQNgRCWGfUjMA@mail.gmail.com>
References: <CABEEk167_xAo6qD7tz=+mH2v5rKXjxkLYp4m4LQNgRCWGfUjMA@mail.gmail.com>
Message-ID: <CAG0CB21BUEtt8WM1AdKAcdAHjCi6wWYDpCiVi9S5kfvNyCn_+g@mail.gmail.com>

Hi Alex,

> I just realized that when clobbering an output file that is a symbolic
> link, several (all?) minc tools will (try to) clobber the target of the
> link instead of the link itself.
>
> I tested this with a few tools (mincaverage, mincmath, mincmorph, minccalc,
> mincresample) and all of them behave this way.

Regardless of if this is a problem or not this behaviour comes about
because of this:

   https://github.com/BIC-MNI/minc/blob/master/libsrc/hdf_convenience.c#L2299

There are ways in HDF of checking if the target is a link.

> IMHO this is actually _really_ bad behaviour; so I was wondering what
> others thought of this, and if this was done by design?

I think you'll find that it was done this way by design, while it's
not the most intuitive thing to do in some cases its (to me) the best
approach to take for all cases. I can think of quite a few scripts of
mine that rely upon this behaviour...

I can also think of a few scripts that don't behave like the library
and instead clobber the link and replace it with a file. The typically
happens like this:

   if( -e $outfile && $clobber){
      system('rm -f $outfile);
      }

   system('stuff $infile $outfile');

a

From alex at bic.mni.mcgill.ca  Mon Mar 18 09:06:35 2013
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Mon, 18 Mar 2013 09:06:35 -0400
Subject: [MINC-users] Of clobbering
In-Reply-To: <CAG0CB21BUEtt8WM1AdKAcdAHjCi6wWYDpCiVi9S5kfvNyCn_+g@mail.gmail.com>
References: <CABEEk167_xAo6qD7tz=+mH2v5rKXjxkLYp4m4LQNgRCWGfUjMA@mail.gmail.com>
	<CAG0CB21BUEtt8WM1AdKAcdAHjCi6wWYDpCiVi9S5kfvNyCn_+g@mail.gmail.com>
Message-ID: <CABEEk17adGWPTj3rcrZoBfSWSvcabaXgOqqCBOtBr_UPuqNd3A@mail.gmail.com>

Hi Andrew,

Regardless of if this is a problem or not this behaviour comes about
> because of this:
>
>
> https://github.com/BIC-MNI/minc/blob/master/libsrc/hdf_convenience.c#L2299
>
> There are ways in HDF of checking if the target is a link.
>

Thanks! So I guess it's therefore pretty much all minc tools that behave
this way. And in fact this seems to be consistent with the default
behaviour of things like 'cp'. Curious. I would argue that a symlink is
analogous to a pointer (as opposed to a reference) in C, so that modifying
the pointer itself should not modify what it points to (unless explicitly
asked); but obviously that doesn't seem to be how it's seen in general.

I can also think of a few scripts that don't behave like the library
> and instead clobber the link and replace it with a file. The typically
> happens like this:
>
>    if( -e $outfile && $clobber){
>       system('rm -f $outfile);
>       }
>
>    system('stuff $infile $outfile');
>

Yes pretty much every script I've ever written does this, and I use it to
my advantage. For example, I use symlinks as space-saving copies for
running pipeline experiments - so I won't need to replicate terabytes of
data for testing the effect of a parameter change in the middle of a
pipeline; but in that setting I definitely don't want to modify my source
tree.

In any event, I go back to making sure I clobber everything explicitly
beforehand :)

-- A

From michal.povazan at meduniwien.ac.at  Tue Mar 19 12:12:32 2013
From: michal.povazan at meduniwien.ac.at (Michal Povazan)
Date: Tue, 19 Mar 2013 17:12:32 +0100
Subject: [MINC-users] display - no decode delegate ...
Message-ID: <51488E70.4090205@meduniwien.ac.at>

Dear all,
I am running ubuntu 12.04 and I have encountered a problem when trying 
to use display
after trying to display image.mnc, imagemagick returns the error message:

no decode delegate for this image format `magnitude.mnc' @ 
error/constitute.c/ReadImage/532.

version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16

although I have founded several answers (not connected to minc) how to 
solve this error, I am not really sure what delegate library should I 
download.

thanks for help

Michal

From jason at phenogenomics.ca  Tue Mar 19 12:15:18 2013
From: jason at phenogenomics.ca (Jason Lerch)
Date: Tue, 19 Mar 2013 12:15:18 -0400
Subject: [MINC-users] display - no decode delegate ...
In-Reply-To: <51488E70.4090205@meduniwien.ac.at>
References: <51488E70.4090205@meduniwien.ac.at>
Message-ID: <EA4F6DC1-DC8D-492C-9DE9-DFF6ED90FC2F@phenogenomics.ca>

If you mean to use the MNI's Display program to view MINC files, try Display with a capital D rather than display with a lower case d.

Jason

On 2013-03-19, at 12:12 PM, Michal Povazan <michal.povazan at meduniwien.ac.at> wrote:

> Dear all,
> I am running ubuntu 12.04 and I have encountered a problem when trying to use display
> after trying to display image.mnc, imagemagick returns the error message:
> 
> no decode delegate for this image format `magnitude.mnc' @ error/constitute.c/ReadImage/532.
> 
> version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16
> 
> although I have founded several answers (not connected to minc) how to solve this error, I am not really sure what delegate library should I download.
> 
> thanks for help
> 
> Michal
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From vladimir.fonov at gmail.com  Tue Mar 19 12:16:02 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 19 Mar 2013 12:16:02 -0400
Subject: [MINC-users] display - no decode delegate ...
In-Reply-To: <51488E70.4090205@meduniwien.ac.at>
References: <51488E70.4090205@meduniwien.ac.at>
Message-ID: <51488F42.3060402@gmail.com>

Hello,

try running Display image.mnc
(with capital D)

On 13-03-19 12:12 PM, Michal Povazan wrote:
> Dear all,
> I am running ubuntu 12.04 and I have encountered a problem when trying
> to use display
> after trying to display image.mnc, imagemagick returns the error message:
>
> no decode delegate for this image format `magnitude.mnc' @
> error/constitute.c/ReadImage/532.
>
> version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16
>
> although I have founded several answers (not connected to minc) how to
> solve this error, I am not really sure what delegate library should I
> download.
>
> thanks for help
>
> Michal
> _______________________________________________
> 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 sorench at gmail.com  Tue Mar 19 12:16:19 2013
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 20 Mar 2013 03:16:19 +1100
Subject: [MINC-users] display - no decode delegate ...
In-Reply-To: <51488E70.4090205@meduniwien.ac.at>
References: <51488E70.4090205@meduniwien.ac.at>
Message-ID: <CAHfsrRYEpGErgXLHErRwXfp5vZtMiy_89prRxEo2emMqHN9ehA@mail.gmail.com>

Sounds like you need a capital D in Display!
On Mar 19, 2013 9:13 AM, "Michal Povazan" <michal.povazan at meduniwien.ac.at>
wrote:

> Dear all,
> I am running ubuntu 12.04 and I have encountered a problem when trying to
> use display
> after trying to display image.mnc, imagemagick returns the error message:
>
> no decode delegate for this image format `magnitude.mnc' @
> error/constitute.c/ReadImage/**532.
>
> version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16
>
> although I have founded several answers (not connected to minc) how to
> solve this error, I am not really sure what delegate library should I
> download.
>
> thanks for help
>
> Michal
> ______________________________**_________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
>

From claude at bic.mni.mcgill.ca  Tue Mar 19 12:19:23 2013
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 19 Mar 2013 12:19:23 -0400
Subject: [MINC-users] display - no decode delegate ...
In-Reply-To: <51488E70.4090205@meduniwien.ac.at>
Message-ID: <201303191619.r2JGJNpY009460@agrippa.bic.mni.mcgill.ca>

Try Display with uppercase D.

>
> Dear all,
> I am running ubuntu 12.04 and I have encountered a problem when trying 
> to use display
> after trying to display image.mnc, imagemagick returns the error message:
>
> no decode delegate for this image format `magnitude.mnc' @ 
> error/constitute.c/ReadImage/532.
>
> version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16
>
> although I have founded several answers (not connected to minc) how to 
> solve this error, I am not really sure what delegate library should I 
> download.
>
> thanks for help
>
> Michal
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Wed Mar 20 13:43:04 2013
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 20 Mar 2013 13:43:04 -0400
Subject: [MINC-users] mincresample and slice-based scaling
Message-ID: <CABEEk17fvz_1k0r0ACkEpSp5VfchO_qL+=3DGTJ0_8DcqAbUSQ@mail.gmail.com>

Hi all,

I came across something somewhat unexpected (at least to me), and was
wondering if anybody would be able to clarify this:

I have a volume with a real range [0,255] (signed short, the valid
range=full range of data type, no slice scaling). When I mincresample that
using a linear xfm and some new starts and steps, I end up with a global
range (from mincstats) of [-0.0002770616653,255.0002071]. I am used to
seeing over- and undershoots with tricubic interpolation, but I was always
under the impression that trilinear by definition should maintain the
extrema. When I add the -keep_real_range flag to the mincresample call, the
resulting range is the expected [0,255] (again from mincstats); so this
essentially fixes the problem. But why would the voxel range change when
using trilinear interpolation? Precision issues? Slice scaling issues?
Extrapolation instead of interpolation perhaps?

-- A

From a.janke at gmail.com  Wed Mar 20 16:03:45 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 21 Mar 2013 06:03:45 +1000
Subject: [MINC-users] mincresample and slice-based scaling
In-Reply-To: <CABEEk17fvz_1k0r0ACkEpSp5VfchO_qL+=3DGTJ0_8DcqAbUSQ@mail.gmail.com>
References: <CABEEk17fvz_1k0r0ACkEpSp5VfchO_qL+=3DGTJ0_8DcqAbUSQ@mail.gmail.com>
Message-ID: <CAG0CB23tB1j6OmeW9Vygi6_zT3ZJHgAw8Vn5C7PF6DF8S_ZQxQ@mail.gmail.com>

Hi Alex,

My guess is that this is a combination of discretisation (of your
chosen data type) and the macros hidden deep within MINC that do the
tri-linear interpolation. Probably more of the former than the latter
though.

Does the same problem happen when you use a float/double volume?

In any case the discretisation is very minimal and I'd say within
expected values given the range of a short (5 places of precision)
matches the error you are seeing.


a

On 21 March 2013 03:43, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hi all,
>
> I came across something somewhat unexpected (at least to me), and was
> wondering if anybody would be able to clarify this:
>
> I have a volume with a real range [0,255] (signed short, the valid
> range=full range of data type, no slice scaling). When I mincresample that
> using a linear xfm and some new starts and steps, I end up with a global
> range (from mincstats) of [-0.0002770616653,255.0002071]. I am used to
> seeing over- and undershoots with tricubic interpolation, but I was always
> under the impression that trilinear by definition should maintain the
> extrema. When I add the -keep_real_range flag to the mincresample call, the
> resulting range is the expected [0,255] (again from mincstats); so this
> essentially fixes the problem. But why would the voxel range change when
> using trilinear interpolation? Precision issues? Slice scaling issues?
> Extrapolation instead of interpolation perhaps?
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From zijdenbos at gmail.com  Wed Mar 20 18:35:52 2013
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 20 Mar 2013 18:35:52 -0400
Subject: [MINC-users] mincresample and slice-based scaling
In-Reply-To: <CAG0CB23tB1j6OmeW9Vygi6_zT3ZJHgAw8Vn5C7PF6DF8S_ZQxQ@mail.gmail.com>
References: <CABEEk17fvz_1k0r0ACkEpSp5VfchO_qL+=3DGTJ0_8DcqAbUSQ@mail.gmail.com>
	<CAG0CB23tB1j6OmeW9Vygi6_zT3ZJHgAw8Vn5C7PF6DF8S_ZQxQ@mail.gmail.com>
Message-ID: <CABEEk15VCwaZQjxhPFV=YF12Q2QXoO3UWByO8ucLnSB0g_H=7g@mail.gmail.com>

Hi Andrew,

I ran a few more tests:

1) mincresample -float, to generate float output
2) convert the input volume to float first
3) combination of the two options above

in all cases the result is the same expanded output range. Also in all
cases the float output volume has the slice scaling ranges set (that may be
fixed in a subsequent MINC releases I assume, following the discussion on
minc-development).

So I would assume that points towards the actual trilinear interpolation,
not discretization, no?

-- A



On Wed, Mar 20, 2013 at 4:03 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Alex,
>
> My guess is that this is a combination of discretisation (of your
> chosen data type) and the macros hidden deep within MINC that do the
> tri-linear interpolation. Probably more of the former than the latter
> though.
>
> Does the same problem happen when you use a float/double volume?
>
> In any case the discretisation is very minimal and I'd say within
> expected values given the range of a short (5 places of precision)
> matches the error you are seeing.
>
>
> a
>
> On 21 March 2013 03:43, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> > Hi all,
> >
> > I came across something somewhat unexpected (at least to me), and was
> > wondering if anybody would be able to clarify this:
> >
> > I have a volume with a real range [0,255] (signed short, the valid
> > range=full range of data type, no slice scaling). When I mincresample
> that
> > using a linear xfm and some new starts and steps, I end up with a global
> > range (from mincstats) of [-0.0002770616653,255.0002071]. I am used to
> > seeing over- and undershoots with tricubic interpolation, but I was
> always
> > under the impression that trilinear by definition should maintain the
> > extrema. When I add the -keep_real_range flag to the mincresample call,
> the
> > resulting range is the expected [0,255] (again from mincstats); so this
> > essentially fixes the problem. But why would the voxel range change when
> > using trilinear interpolation? Precision issues? Slice scaling issues?
> > Extrapolation instead of interpolation perhaps?
> >
> > -- 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 michal.povazan at meduniwien.ac.at  Thu Mar 21 05:23:19 2013
From: michal.povazan at meduniwien.ac.at (Michal Povazan)
Date: Thu, 21 Mar 2013 10:23:19 +0100
Subject: [MINC-users] display - no decode delegate ...
In-Reply-To: <51488E70.4090205@meduniwien.ac.at>
References: <51488E70.4090205@meduniwien.ac.at>
Message-ID: <514AD187.6000005@meduniwien.ac.at>

I am blushing, you are right, thanks for the answer

Michal

On 03/19/2013 05:12 PM, Michal Povazan wrote:
> Dear all,
> I am running ubuntu 12.04 and I have encountered a problem when trying 
> to use display
> after trying to display image.mnc, imagemagick returns the error message:
>
> no decode delegate for this image format `magnitude.mnc' @ 
> error/constitute.c/ReadImage/532.
>
> version of imagemagick is : ImageMagick 6.6.9-7 2012-08-17 Q16
>
> although I have founded several answers (not connected to minc) how to 
> solve this error, I am not really sure what delegate library should I 
> download.
>
> thanks for help
>
> Michal


From winterburn.julie at gmail.com  Mon Mar 25 11:50:25 2013
From: winterburn.julie at gmail.com (Julie Winterburn)
Date: Mon, 25 Mar 2013 11:50:25 -0400
Subject: [MINC-users] MINC to NIfTI label file conversion
Message-ID: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>

Hi,

I am having a problem converting MINC label files to NIfTI. The label file
in MINC format has integer values (1,2, etc). I am using <mnc2nii -short>
to convert, but when viewing the label file in fslview, the values are
non-integer (0.831373, 2.07843, etc.). The output is the same for <mnc2nii
-int>. Is there a way to maintain the values as integers in NIfTI?

Thanks,
Julie

From eskild at gmail.com  Mon Mar 25 13:14:47 2013
From: eskild at gmail.com (Simon Eskildsen)
Date: Mon, 25 Mar 2013 18:14:47 +0100
Subject: [MINC-users] MINC to NIfTI label file conversion
In-Reply-To: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>
References: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>
Message-ID: <CAD3v437wSARS3Wwsh_AvupdA3bjO3zOwxKM0_8JctSZcTFYr4Q@mail.gmail.com>

Hi Julie,

When converting from minc to nifti, I always do mincreshape -float before
calling mnc2nii in order to avoid problems of intensity scaling.
Perhaps this solves your problem?

Simon

On Mon, Mar 25, 2013 at 4:50 PM, Julie Winterburn <
winterburn.julie at gmail.com> wrote:

> Hi,
>
> I am having a problem converting MINC label files to NIfTI. The label file
> in MINC format has integer values (1,2, etc). I am using <mnc2nii -short>
> to convert, but when viewing the label file in fslview, the values are
> non-integer (0.831373, 2.07843, etc.). The output is the same for <mnc2nii
> -int>. Is there a way to maintain the values as integers in NIfTI?
>
> Thanks,
> Julie
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From winterburn.julie at gmail.com  Mon Mar 25 14:17:22 2013
From: winterburn.julie at gmail.com (Julie Winterburn)
Date: Mon, 25 Mar 2013 14:17:22 -0400
Subject: [MINC-users] MINC to NIfTI label file conversion
In-Reply-To: <CAD3v437wSARS3Wwsh_AvupdA3bjO3zOwxKM0_8JctSZcTFYr4Q@mail.gmail.com>
References: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>
	<CAD3v437wSARS3Wwsh_AvupdA3bjO3zOwxKM0_8JctSZcTFYr4Q@mail.gmail.com>
Message-ID: <CADkSHQRVKyFuHXk2yfaADPsqxkrWZz60EJsNbOkSDu3L2wrK3A@mail.gmail.com>

Thanks, that helps a lot! The only problem now is that not *all* of the
label values end up as integers. For example, in a label set with intended
values 1, 2, 4, 5, 6, the NIfTI file contains values 1.01176, 2, 4,
5.01176, 6.  Any idea why this might still be happening to only a few of
the numbers?

On 25 March 2013 13:14, Simon Eskildsen <eskild at gmail.com> wrote:

> Hi Julie,
>
> When converting from minc to nifti, I always do mincreshape -float before
> calling mnc2nii in order to avoid problems of intensity scaling.
> Perhaps this solves your problem?
>
> Simon
>
> On Mon, Mar 25, 2013 at 4:50 PM, Julie Winterburn <
> winterburn.julie at gmail.com> wrote:
>
> > Hi,
> >
> > I am having a problem converting MINC label files to NIfTI. The label
> file
> > in MINC format has integer values (1,2, etc). I am using <mnc2nii -short>
> > to convert, but when viewing the label file in fslview, the values are
> > non-integer (0.831373, 2.07843, etc.). The output is the same for
> <mnc2nii
> > -int>. Is there a way to maintain the values as integers in NIfTI?
> >
> > Thanks,
> > Julie
> > _______________________________________________
> > 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 a.janke at gmail.com  Mon Mar 25 18:50:20 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 26 Mar 2013 08:50:20 +1000
Subject: [MINC-users] MINC to NIfTI label file conversion
In-Reply-To: <CADkSHQRVKyFuHXk2yfaADPsqxkrWZz60EJsNbOkSDu3L2wrK3A@mail.gmail.com>
References: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>
	<CAD3v437wSARS3Wwsh_AvupdA3bjO3zOwxKM0_8JctSZcTFYr4Q@mail.gmail.com>
	<CADkSHQRVKyFuHXk2yfaADPsqxkrWZz60EJsNbOkSDu3L2wrK3A@mail.gmail.com>
Message-ID: <CAG0CB21t7U1OVxBJZDK-hAbdp7V2O9eh=736+h5Ox-pg04qKiQ@mail.gmail.com>

Hi Julie,

This should be simple buy it unfortunately depends on what you are
using to read the nifti files. Are you attempting to use them in FSL
or SPM or something else entirely?

a



On 26 March 2013 04:17, Julie Winterburn <winterburn.julie at gmail.com> wrote:
> Thanks, that helps a lot! The only problem now is that not *all* of the
> label values end up as integers. For example, in a label set with intended
> values 1, 2, 4, 5, 6, the NIfTI file contains values 1.01176, 2, 4,
> 5.01176, 6.  Any idea why this might still be happening to only a few of
> the numbers?

From winterburn.julie at gmail.com  Tue Mar 26 10:51:24 2013
From: winterburn.julie at gmail.com (Julie Winterburn)
Date: Tue, 26 Mar 2013 10:51:24 -0400
Subject: [MINC-users] MINC to NIfTI label file conversion
In-Reply-To: <CAG0CB21t7U1OVxBJZDK-hAbdp7V2O9eh=736+h5Ox-pg04qKiQ@mail.gmail.com>
References: <CADkSHQRjE3zuViRDsw+aKbo8LDyag+FtSXXftwW3Ccqioob8Jw@mail.gmail.com>
	<CAD3v437wSARS3Wwsh_AvupdA3bjO3zOwxKM0_8JctSZcTFYr4Q@mail.gmail.com>
	<CADkSHQRVKyFuHXk2yfaADPsqxkrWZz60EJsNbOkSDu3L2wrK3A@mail.gmail.com>
	<CAG0CB21t7U1OVxBJZDK-hAbdp7V2O9eh=736+h5Ox-pg04qKiQ@mail.gmail.com>
Message-ID: <CADkSHQTRmPdAdF1C8EYxpPqwYh8Kaw7kike4Gd-61jFCzSmmyA@mail.gmail.com>

I'm using fslview.

On 25 March 2013 18:50, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Julie,
>
> This should be simple buy it unfortunately depends on what you are
> using to read the nifti files. Are you attempting to use them in FSL
> or SPM or something else entirely?
>
> a
>
>
>
> On 26 March 2013 04:17, Julie Winterburn <winterburn.julie at gmail.com>
> wrote:
> > Thanks, that helps a lot! The only problem now is that not *all* of the
> > label values end up as integers. For example, in a label set with
> intended
> > values 1, 2, 4, 5, 6, the NIfTI file contains values 1.01176, 2, 4,
> > 5.01176, 6.  Any idea why this might still be happening to only a few of
> > the numbers?
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>