From trash001 at odu.edu  Fri Nov  1 12:08:26 2013
From: trash001 at odu.edu (Tanweer Rashid)
Date: Fri, 1 Nov 2013 12:08:26 -0400
Subject: [MINC-users] mincblur output filetype
Message-ID: <CAE1j2uhBD0tLKP-WWDyjTMdjYv-7jo8rB_ibDSgqrAtaSvYD5A@mail.gmail.com>

Hi,

I was wondering how I can keep the format (i.e. datatype, range, etc) of
the output file the same as the input file when using mincblur.

-- 
Tanweer Rashid
MSVE Dept.
Old Dominion University

From vladimir.fonov at gmail.com  Fri Nov  1 13:14:17 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 1 Nov 2013 13:14:17 -0400
Subject: [MINC-users] mincblur output filetype
In-Reply-To: <CAE1j2uhBD0tLKP-WWDyjTMdjYv-7jo8rB_ibDSgqrAtaSvYD5A@mail.gmail.com>
References: <CAE1j2uhBD0tLKP-WWDyjTMdjYv-7jo8rB_ibDSgqrAtaSvYD5A@mail.gmail.com>
Message-ID: <CAMCwi7O7RCWN5eG_TrrZmEsMz819sLOiftaqz=AAJdX0HxyZ8g@mail.gmail.com>

Hello,

I think that's what it tries to do by default, except that it
recalculates image range

On Fri, Nov 1, 2013 at 12:08 PM, Tanweer Rashid <trash001 at odu.edu> wrote:
> Hi,
>
> I was wondering how I can keep the format (i.e. datatype, range, etc) of
> the output file the same as the input file when using mincblur.
>
> --
> Tanweer Rashid
> MSVE Dept.
> Old Dominion University
> _______________________________________________
> 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 trash001 at odu.edu  Fri Nov 15 12:13:24 2013
From: trash001 at odu.edu (Tanweer Rashid)
Date: Fri, 15 Nov 2013 12:13:24 -0500
Subject: [MINC-users] Range of values that can be set with
	miset_voxel_value()
Message-ID: <CAE1j2uh_ASsSthrnByK_BmFv8JFLvoE6Uy=dqSsVe3DqTmLeAA@mail.gmail.com>

Hi,

I am trying to figure out the range of values that can be set in a minc
file using the miset_voxel_value() function. Right now, that range seems to
be 0 to 1. Is this correct?

Also, is there any way to set values less than 0 or greater than 1?

Thanks,
-- 
Tanweer Rashid
MSVE Dept.
Old Dominion University

From sorench at gmail.com  Fri Nov 15 12:39:45 2013
From: sorench at gmail.com (Soren Christensen)
Date: Fri, 15 Nov 2013 09:39:45 -0800
Subject: [MINC-users] Range of values that can be set with
	miset_voxel_value()
In-Reply-To: <CAE1j2uh_ASsSthrnByK_BmFv8JFLvoE6Uy=dqSsVe3DqTmLeAA@mail.gmail.com>
References: <CAE1j2uh_ASsSthrnByK_BmFv8JFLvoE6Uy=dqSsVe3DqTmLeAA@mail.gmail.com>
Message-ID: <CAHfsrRaDnC9=ZyFR2qtW2vg1Zs4Y95+ZrwSC4M3SjCo+JYcxSQ@mail.gmail.com>

At least when using

miset_voxel_value_hyperslab

you can set any value you want within the data type specified.


>From the documentation to miset_voxel_value:

 This function sets the voxel value of a position in the MINC
 volume.  The voxel value is the unscaled value, and corresponds to the
 value actually stored in the file.

It would not seem it is constrained to 0-1.    If you read the location
back out with the corresponding get, don't you get the value you put in?

Soren


On Fri, Nov 15, 2013 at 9:13 AM, Tanweer Rashid <trash001 at odu.edu> wrote:

> Hi,
>
> I am trying to figure out the range of values that can be set in a minc
> file using the miset_voxel_value() function. Right now, that range seems to
> be 0 to 1. Is this correct?
>
> Also, is there any way to set values less than 0 or greater than 1?
>
> Thanks,
> --
> Tanweer Rashid
> MSVE Dept.
> Old Dominion University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sanabria.sandra at gene.com  Fri Nov 15 17:07:10 2013
From: sanabria.sandra at gene.com (Sandra Sanabria)
Date: Fri, 15 Nov 2013 14:07:10 -0800
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
Message-ID: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>

Hello,
I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
Any help with this will be very appreciated!

Thanks,

Sandra

From vladimir.fonov at gmail.com  Fri Nov 15 17:19:35 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 15 Nov 2013 17:19:35 -0500
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>
Message-ID: <52869DF7.208@gmail.com>

Hello,

did you run execute source /opt/minc/minc-toolkit-config.sh
command before trying to run rawtominc ?

On 13-11-15 05:07 PM, Sandra Sanabria wrote:
> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
> Any help with this will be very appreciated!


-- 
Best regards,

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

From sanabria.sandra at gene.com  Fri Nov 15 17:36:29 2013
From: sanabria.sandra at gene.com (Sandra Sanabria)
Date: Fri, 15 Nov 2013 14:36:29 -0800
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <52869DF7.208@gmail.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>
	<52869DF7.208@gmail.com>
Message-ID: <0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>

Yes, I did. Should I set any other env variable or add any other folder to the path?

Thank you

Sandra

Enviado desde mi iPhone

> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
> 
> Hello,
> 
> did you run execute source /opt/minc/minc-toolkit-config.sh
> command before trying to run rawtominc ?
> 
>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>> Any help with this will be very appreciated!
> 
> 
> -- 
> 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 Nov 15 18:22:09 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 15 Nov 2013 18:22:09 -0500
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>	<52869DF7.208@gmail.com>
	<0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>
Message-ID: <5286ACA1.2080308@gmail.com>

Hello,

what's the output of

which rawtominc
and
otool -L /opt/minc/bin/rawtominc

?


On 13-11-15 05:36 PM, Sandra Sanabria wrote:
> Yes, I did. Should I set any other env variable or add any other folder to the path?
>
> Thank you
>
> Sandra
>
> Enviado desde mi iPhone
>
>> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
>>
>> Hello,
>>
>> did you run execute source /opt/minc/minc-toolkit-config.sh
>> command before trying to run rawtominc ?
>>
>>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>>> Any help with this will be very appreciated!
>>
>>
>> --
>> 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 Nov 15 23:17:19 2013
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 15 Nov 2013 23:17:19 -0500
Subject: [MINC-users] mincstats histogram count limit?
Message-ID: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>

Hello all,

I seem to have stumbled across a limit to the histogram counts in
mincstats. I thought it may be a data type limitation, but going through
the source code I so far haven't been able to find a cause.

I have a classified, discrete volume only containing values 1, 2, and 3;
it's a 722x866x722 volume with 0.25mm isotropic voxels. To get the voxel
counts for each of the labels in the volume:

$ mincstats -clobber -quiet -none -integer_histogram -hist_range 1 3
-histogram hr_hist.txt hr.mnc
451431944
$ cat hr_hist.txt
# histogram for: hr.mnc
#  mask file:    (null)
#  domain:       0.5  3.5
#  entropy:      1.32723
# bin centres                 counts
  1                      1.67322e+07
  2                      1.67772e+07
  3                      1.67772e+07

However:

$ mincstats -clobber -none -count -binvalue 1,2,3 hr.mnc
Included Range:    0.5   1.5
# voxels:          16732212
Included Range:    1.5   2.5
# voxels:          42817611
Included Range:    2.5   3.5
# voxels:          35033439

The red and green results _should_ be the same; but in the histogram output
the seem to be capped at 1.67772e+07, which is clearly wrong.

Anybody able to figure this out?

Thanks,

-- A

From vladimir.fonov at gmail.com  Fri Nov 15 23:44:34 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 15 Nov 2013 23:44:34 -0500
Subject: [MINC-users] mincstats histogram count limit?
In-Reply-To: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
References: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
Message-ID: <CA532A19-666B-420D-9D64-AD14A7211CF6@gmail.com>

Hello,


what about print_all_labels ? 

On 2013-11-15, at 11:17 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hello all,
> 
> I seem to have stumbled across a limit to the histogram counts in
> mincstats. I thought it may be a data type limitation, but going through
> the source code I so far haven't been able to find a cause.
> 
> I have a classified, discrete volume only containing values 1, 2, and 3;
> it's a 722x866x722 volume with 0.25mm isotropic voxels. To get the voxel
> counts for each of the labels in the volume:
> 
> $ mincstats -clobber -quiet -none -integer_histogram -hist_range 1 3
> -histogram hr_hist.txt hr.mnc
> 451431944
> $ cat hr_hist.txt
> # histogram for: hr.mnc
> #  mask file:    (null)
> #  domain:       0.5  3.5
> #  entropy:      1.32723
> # bin centres                 counts
>  1                      1.67322e+07
>  2                      1.67772e+07
>  3                      1.67772e+07
> 
> However:
> 
> $ mincstats -clobber -none -count -binvalue 1,2,3 hr.mnc
> Included Range:    0.5   1.5
> # voxels:          16732212
> Included Range:    1.5   2.5
> # voxels:          42817611
> Included Range:    2.5   3.5
> # voxels:          35033439
> 
> The red and green results _should_ be the same; but in the histogram output
> the seem to be capped at 1.67772e+07, which is clearly wrong.
> 
> Anybody able to figure this out?
> 
> Thanks,
> 
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

---
Best regards,

Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info






From zijdenbos at gmail.com  Sat Nov 16 00:08:31 2013
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 16 Nov 2013 00:08:31 -0500
Subject: [MINC-users] mincstats histogram count limit?
In-Reply-To: <CA532A19-666B-420D-9D64-AD14A7211CF6@gmail.com>
References: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
	<CA532A19-666B-420D-9D64-AD14A7211CF6@gmail.com>
Message-ID: <CABEEk17TNgYFMobkzRc3_c+pPirLjKf=OXbLt6ZzcpPR-O1fqQ@mail.gmail.com>

Hi Vladimir,

print_all_labels gives the same (correct) result as mincstats -count
-binvalue label,label,.... (green values). It only seems to be the counts
in minstats' histogram that are off.

By the way, these counts are printed in the histogram using %12g - that
shouldn't cap them at 1.67772e+07 I would think, but either way they should
probably be printed as integers.

-- A


On Fri, Nov 15, 2013 at 11:44 PM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> Hello,
>
>
> what about print_all_labels ?
>
> On 2013-11-15, at 11:17 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
> > Hello all,
> >
> > I seem to have stumbled across a limit to the histogram counts in
> > mincstats. I thought it may be a data type limitation, but going through
> > the source code I so far haven't been able to find a cause.
> >
> > I have a classified, discrete volume only containing values 1, 2, and 3;
> > it's a 722x866x722 volume with 0.25mm isotropic voxels. To get the voxel
> > counts for each of the labels in the volume:
> >
> > $ mincstats -clobber -quiet -none -integer_histogram -hist_range 1 3
> > -histogram hr_hist.txt hr.mnc
> > 451431944
> > $ cat hr_hist.txt
> > # histogram for: hr.mnc
> > #  mask file:    (null)
> > #  domain:       0.5  3.5
> > #  entropy:      1.32723
> > # bin centres                 counts
> >  1                      1.67322e+07
> >  2                      1.67772e+07
> >  3                      1.67772e+07
> >
> > However:
> >
> > $ mincstats -clobber -none -count -binvalue 1,2,3 hr.mnc
> > Included Range:    0.5   1.5
> > # voxels:          16732212
> > Included Range:    1.5   2.5
> > # voxels:          42817611
> > Included Range:    2.5   3.5
> > # voxels:          35033439
> >
> > The red and green results _should_ be the same; but in the histogram
> output
> > the seem to be capped at 1.67772e+07, which is clearly wrong.
> >
> > Anybody able to figure this out?
> >
> > Thanks,
> >
> > -- A
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> ---
> Best regards,
>
> Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info
>
>
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From a.janke at gmail.com  Sat Nov 16 00:29:16 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 15 Nov 2013 21:29:16 -0800
Subject: [MINC-users] mincstats histogram count limit?
In-Reply-To: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
References: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
Message-ID: <CAG0CB23-iOP9CEkFGeviH20ZCKsKOxeaB8tABopMUz31UHDXCw@mail.gmail.com>

On 15 November 2013 20:17, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> $ mincstats -clobber -quiet -none -integer_histogram -hist_range 1 3
> -histogram hr_hist.txt hr.mnc
> 451431944
> $ cat hr_hist.txt
> # histogram for: hr.mnc
> #  mask file:    (null)
> #  domain:       0.5  3.5
> #  entropy:      1.32723
> # bin centres                 counts
>   1                      1.67322e+07
>   2                      1.67772e+07
>   3                      1.67772e+07
>
> However:
>
> $ mincstats -clobber -none -count -binvalue 1,2,3 hr.mnc
> Included Range:    0.5   1.5
> # voxels:          16732212
> Included Range:    1.5   2.5
> # voxels:          42817611
> Included Range:    2.5   3.5
> # voxels:          35033439
>
> The red and green results _should_ be the same; but in the histogram output
> the seem to be capped at 1.67772e+07, which is clearly wrong.
>
> Anybody able to figure this out?

Strange..

This looks to me more like a memory error in that only the first count
is printed, the histogram range calculation has always been a bit of
black magic that made sense at the time it was written! and then Peter
and Bert both had a go at adding things to it.

For some reason I also note that the histogram array is a float and
everything else is double. Is there a chance that this is a cast
problem that only shows up on 64 bit?  Can you change line 154:

   https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L154

To double and test?


a

From sanabria.sandra at gene.com  Mon Nov 18 03:10:00 2013
From: sanabria.sandra at gene.com (Sandra Sanabria)
Date: Mon, 18 Nov 2013 00:10:00 -0800
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <5286ACA1.2080308@gmail.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>	<52869DF7.208@gmail.com>
	<0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>
	<5286ACA1.2080308@gmail.com>
Message-ID: <AA4F04F6-4313-4AE8-AC2B-FC6D8639BA82@gene.com>

Hello,

$ which rawtominc
/opt/minc/bin/rawtominc


$ otool -L /opt/minc/bin/rawtominc
/opt/minc/bin/rawtominc:
	libminc2.2.dylib (compatibility version 2.0.0, current version 2.2.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

This is the fool message when trying to use rawtominc:
$ rawtominc -input tmpfile.img -ofloat -transverse -float  -xstep 1.084170 -ystep 1.084170 -zstep 1.211500 tmpfile.mnc 1 63 128 128 -range 0 3.398243
dyld: Library not loaded: libminc2.2.dylib
  Referenced from: /opt/minc/bin/rawtominc
  Reason: image not found
Trace/BPT trap: 5

Thanks,
S
On Nov 15, 2013, at 3:22 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello,
> 
> what's the output of
> 
> which rawtominc
> and
> otool -L /opt/minc/bin/rawtominc
> 
> ?
> 
> 
> On 13-11-15 05:36 PM, Sandra Sanabria wrote:
>> Yes, I did. Should I set any other env variable or add any other folder to the path?
>> 
>> Thank you
>> 
>> Sandra
>> 
>> Enviado desde mi iPhone
>> 
>>> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
>>> 
>>> Hello,
>>> 
>>> did you run execute source /opt/minc/minc-toolkit-config.sh
>>> command before trying to run rawtominc ?
>>> 
>>>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>>>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>>>> Any help with this will be very appreciated!
>>> 
>>> 
>>> --
>>> 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  Mon Nov 18 12:09:54 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 18 Nov 2013 12:09:54 -0500
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <AA4F04F6-4313-4AE8-AC2B-FC6D8639BA82@gene.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>	<52869DF7.208@gmail.com>	<0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>	<5286ACA1.2080308@gmail.com>
	<AA4F04F6-4313-4AE8-AC2B-FC6D8639BA82@gene.com>
Message-ID: <528A49E2.9000500@gmail.com>

Ok,


what about DYLD_LIBRARY_PATH environment variable, what does

echo $DYLD_LIBRARY_PATH shows?



On 13-11-18 03:10 AM, Sandra Sanabria wrote:
> Hello,
>
> $ which rawtominc
> /opt/minc/bin/rawtominc
>
>
> $ otool -L /opt/minc/bin/rawtominc
> /opt/minc/bin/rawtominc:
> 	libminc2.2.dylib (compatibility version 2.0.0, current version 2.2.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)
>
> This is the fool message when trying to use rawtominc:
> $ rawtominc -input tmpfile.img -ofloat -transverse -float  -xstep 1.084170 -ystep 1.084170 -zstep 1.211500 tmpfile.mnc 1 63 128 128 -range 0 3.398243
> dyld: Library not loaded: libminc2.2.dylib
>    Referenced from: /opt/minc/bin/rawtominc
>    Reason: image not found
> Trace/BPT trap: 5
>
> Thanks,
> S
> On Nov 15, 2013, at 3:22 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>
>> Hello,
>>
>> what's the output of
>>
>> which rawtominc
>> and
>> otool -L /opt/minc/bin/rawtominc
>>
>> ?
>>
>>
>> On 13-11-15 05:36 PM, Sandra Sanabria wrote:
>>> Yes, I did. Should I set any other env variable or add any other folder to the path?
>>>
>>> Thank you
>>>
>>> Sandra
>>>
>>> Enviado desde mi iPhone
>>>
>>>> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
>>>>
>>>> Hello,
>>>>
>>>> did you run execute source /opt/minc/minc-toolkit-config.sh
>>>> command before trying to run rawtominc ?
>>>>
>>>>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>>>>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>>>>> Any help with this will be very appreciated!
>>>>
>>>>
>>>> --
>>>> 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 sanabria.sandra at gene.com  Mon Nov 18 14:16:13 2013
From: sanabria.sandra at gene.com (Sandra Sanabria)
Date: Mon, 18 Nov 2013 11:16:13 -0800
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <528A49E2.9000500@gmail.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>	<52869DF7.208@gmail.com>	<0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>	<5286ACA1.2080308@gmail.com>
	<AA4F04F6-4313-4AE8-AC2B-FC6D8639BA82@gene.com>
	<528A49E2.9000500@gmail.com>
Message-ID: <EAF942BB-70E9-458D-A8E2-F605008908A7@gene.com>

It was empty, I set it to:
DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/minc/lib:/opt/minc/lib/InsightToolkit

(not sure why if I  run execute source /opt/minc/minc-toolkit-config.sh)

I can use rawtominc but, although display opens, it dies when opening the file:

display test.mnc
Input test.mnc
Objects input.
display(90923,0x7fff736e1180) malloc: *** mmap(size=18446744065119621120) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error reallocing -2147482740 elements of size 4.
    Source position: /Users/vfonov/src/minc-toolkit/bicpl/Numerical/histogram.c:174
Segmentation fault: 11


(I wish I hadn?t gone Mountain Lion!)

Thanks



On Nov 18, 2013, at 9:09 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Ok,
> 
> 
> what about DYLD_LIBRARY_PATH environment variable, what does
> 
> echo $DYLD_LIBRARY_PATH shows?
> 
> 
> 
> On 13-11-18 03:10 AM, Sandra Sanabria wrote:
>> Hello,
>> 
>> $ which rawtominc
>> /opt/minc/bin/rawtominc
>> 
>> 
>> $ otool -L /opt/minc/bin/rawtominc
>> /opt/minc/bin/rawtominc:
>> 	libminc2.2.dylib (compatibility version 2.0.0, current version 2.2.0)
>> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)
>> 
>> This is the fool message when trying to use rawtominc:
>> $ rawtominc -input tmpfile.img -ofloat -transverse -float  -xstep 1.084170 -ystep 1.084170 -zstep 1.211500 tmpfile.mnc 1 63 128 128 -range 0 3.398243
>> dyld: Library not loaded: libminc2.2.dylib
>>   Referenced from: /opt/minc/bin/rawtominc
>>   Reason: image not found
>> Trace/BPT trap: 5
>> 
>> Thanks,
>> S
>> On Nov 15, 2013, at 3:22 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>> 
>>> Hello,
>>> 
>>> what's the output of
>>> 
>>> which rawtominc
>>> and
>>> otool -L /opt/minc/bin/rawtominc
>>> 
>>> ?
>>> 
>>> 
>>> On 13-11-15 05:36 PM, Sandra Sanabria wrote:
>>>> Yes, I did. Should I set any other env variable or add any other folder to the path?
>>>> 
>>>> Thank you
>>>> 
>>>> Sandra
>>>> 
>>>> Enviado desde mi iPhone
>>>> 
>>>>> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
>>>>> 
>>>>> Hello,
>>>>> 
>>>>> did you run execute source /opt/minc/minc-toolkit-config.sh
>>>>> command before trying to run rawtominc ?
>>>>> 
>>>>>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>>>>>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>>>>>> Any help with this will be very appreciated!
>>>>> 
>>>>> 
>>>>> --
>>>>> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From vladimir.fonov at gmail.com  Mon Nov 18 15:04:17 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 18 Nov 2013 15:04:17 -0500
Subject: [MINC-users] Library not loaded: libminc2.2.dylib
In-Reply-To: <EAF942BB-70E9-458D-A8E2-F605008908A7@gene.com>
References: <99244C27-3A5E-4B80-B175-18F06DF4C9C7@gene.com>	<52869DF7.208@gmail.com>	<0AA034F0-A0CF-4C0A-BB48-C33B73745EA5@gene.com>	<5286ACA1.2080308@gmail.com>	<AA4F04F6-4313-4AE8-AC2B-FC6D8639BA82@gene.com>	<528A49E2.9000500@gmail.com>
	<EAF942BB-70E9-458D-A8E2-F605008908A7@gene.com>
Message-ID: <528A72C1.4010303@gmail.com>

Hello,

Display usually dies when the volume have zero voxels everywhere.

On 13-11-18 02:16 PM, Sandra Sanabria wrote:
> It was empty, I set it to:
> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/minc/lib:/opt/minc/lib/InsightToolkit
>
> (not sure why if I  run execute source /opt/minc/minc-toolkit-config.sh)
>
> I can use rawtominc but, although display opens, it dies when opening the file:
>
> display test.mnc
> Input test.mnc
> Objects input.
> display(90923,0x7fff736e1180) malloc: *** mmap(size=18446744065119621120) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Error reallocing -2147482740 elements of size 4.
>      Source position: /Users/vfonov/src/minc-toolkit/bicpl/Numerical/histogram.c:174
> Segmentation fault: 11
>
>
> (I wish I hadn?t gone Mountain Lion!)
>
> Thanks
>
>
>
> On Nov 18, 2013, at 9:09 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>
>> Ok,
>>
>>
>> what about DYLD_LIBRARY_PATH environment variable, what does
>>
>> echo $DYLD_LIBRARY_PATH shows?
>>
>>
>>
>> On 13-11-18 03:10 AM, Sandra Sanabria wrote:
>>> Hello,
>>>
>>> $ which rawtominc
>>> /opt/minc/bin/rawtominc
>>>
>>>
>>> $ otool -L /opt/minc/bin/rawtominc
>>> /opt/minc/bin/rawtominc:
>>> 	libminc2.2.dylib (compatibility version 2.0.0, current version 2.2.0)
>>> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)
>>>
>>> This is the fool message when trying to use rawtominc:
>>> $ rawtominc -input tmpfile.img -ofloat -transverse -float  -xstep 1.084170 -ystep 1.084170 -zstep 1.211500 tmpfile.mnc 1 63 128 128 -range 0 3.398243
>>> dyld: Library not loaded: libminc2.2.dylib
>>>    Referenced from: /opt/minc/bin/rawtominc
>>>    Reason: image not found
>>> Trace/BPT trap: 5
>>>
>>> Thanks,
>>> S
>>> On Nov 15, 2013, at 3:22 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> what's the output of
>>>>
>>>> which rawtominc
>>>> and
>>>> otool -L /opt/minc/bin/rawtominc
>>>>
>>>> ?
>>>>
>>>>
>>>> On 13-11-15 05:36 PM, Sandra Sanabria wrote:
>>>>> Yes, I did. Should I set any other env variable or add any other folder to the path?
>>>>>
>>>>> Thank you
>>>>>
>>>>> Sandra
>>>>>
>>>>> Enviado desde mi iPhone
>>>>>
>>>>>> El Nov 15, 2013, a las 14:19, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> escribi?:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> did you run execute source /opt/minc/minc-toolkit-config.sh
>>>>>> command before trying to run rawtominc ?
>>>>>>
>>>>>>> On 13-11-15 05:07 PM, Sandra Sanabria wrote:
>>>>>>> I?m on MAC OSX 10.8.3 and tried to install the MINC Tool Kit following the directions in http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit. However, when I try to run ?rawtominc? I get the following error message: dyld: Library not loaded: libminc2.2.dylib
>>>>>>> Any help with this will be very appreciated!
>>>>>>


-- 
Best regards,

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

From andrew at biospective.com  Mon Nov 25 12:10:37 2013
From: andrew at biospective.com (Andrew Wood)
Date: Mon, 25 Nov 2013 12:10:37 -0500
Subject: [MINC-users] mincstats histogram count limit?
In-Reply-To: <CAG0CB23-iOP9CEkFGeviH20ZCKsKOxeaB8tABopMUz31UHDXCw@mail.gmail.com>
References: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
	<CAG0CB23-iOP9CEkFGeviH20ZCKsKOxeaB8tABopMUz31UHDXCw@mail.gmail.com>
Message-ID: <CABApf9F2gmn0O8rPmg-_4srNG4bPMxCwK=2RvCuBH_8xjoQFAQ@mail.gmail.com>

Hi all,

The problem goes away if the histogram array is changed to double, as AJ
suggested. There are a few other float arrays used in this bit of code: bin
centres, probability density function and cumulative density function. They
don't seem to be causing problems right now, but might it make sense to
change those over to double while I'm at at?

- Andrew


On Sat, Nov 16, 2013 at 12:29 AM, Andrew Janke <a.janke at gmail.com> wrote:

> On 15 November 2013 20:17, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> > $ mincstats -clobber -quiet -none -integer_histogram -hist_range 1 3
> > -histogram hr_hist.txt hr.mnc
> > 451431944
> > $ cat hr_hist.txt
> > # histogram for: hr.mnc
> > #  mask file:    (null)
> > #  domain:       0.5  3.5
> > #  entropy:      1.32723
> > # bin centres                 counts
> >   1                      1.67322e+07
> >   2                      1.67772e+07
> >   3                      1.67772e+07
> >
> > However:
> >
> > $ mincstats -clobber -none -count -binvalue 1,2,3 hr.mnc
> > Included Range:    0.5   1.5
> > # voxels:          16732212
> > Included Range:    1.5   2.5
> > # voxels:          42817611
> > Included Range:    2.5   3.5
> > # voxels:          35033439
> >
> > The red and green results _should_ be the same; but in the histogram
> output
> > the seem to be capped at 1.67772e+07, which is clearly wrong.
> >
> > Anybody able to figure this out?
>
> Strange..
>
> This looks to me more like a memory error in that only the first count
> is printed, the histogram range calculation has always been a bit of
> black magic that made sense at the time it was written! and then Peter
> and Bert both had a go at adding things to it.
>
> For some reason I also note that the histogram array is a float and
> everything else is double. Is there a chance that this is a cast
> problem that only shows up on 64 bit?  Can you change line 154:
>
>
> https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L154
>
> To double and test?
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Mon Nov 25 14:57:33 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 26 Nov 2013 05:57:33 +1000
Subject: [MINC-users] mincstats histogram count limit?
In-Reply-To: <CABApf9F2gmn0O8rPmg-_4srNG4bPMxCwK=2RvCuBH_8xjoQFAQ@mail.gmail.com>
References: <CABEEk17Jx0boaa3syA+KhJHXr7cHRT_zSgisSjJ_66Di67fofg@mail.gmail.com>
	<CAG0CB23-iOP9CEkFGeviH20ZCKsKOxeaB8tABopMUz31UHDXCw@mail.gmail.com>
	<CABApf9F2gmn0O8rPmg-_4srNG4bPMxCwK=2RvCuBH_8xjoQFAQ@mail.gmail.com>
Message-ID: <CAG0CB23ONN6ydVoA0LPhuzyLSE-Lvq=q86J9jP_tkoWEjjFajg@mail.gmail.com>

On 26 November 2013 03:10, Andrew Wood <andrew at biospective.com> wrote:
>
> The problem goes away if the histogram array is changed to double, as AJ
> suggested. There are a few other float arrays used in this bit of code: bin
> centres, probability density function and cumulative density function. They
> don't seem to be causing problems right now, but might it make sense to
> change those over to double while I'm at at?

Yes, I'd change them all to double, if you make the changes and push
to github I'll include them.

Thanks


a