From zijdenbos at gmail.com  Wed Jul  6 10:07:09 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 6 Jul 2016 10:07:09 -0400
Subject: [MINC-users] mincresample -like and -{tfm,use}_input_sampling
Message-ID: <CABEEk16H4ZqyNtxwNGA6UFwLWcTPueRmERVTqqLSN_WoFprmMQ@mail.gmail.com>

Hi all,

I realized that mincresample happily accepts multiple of these options
simultaneously:

-like <model.mnc>
-tfm_input_sampling
-use_input_sampling

I would think that these three options should be mutually exclusive, and
that mincresample should check for that? I believe at the moment, -like
silently takes precedence between these three.

-- A

From zijdenbos at gmail.com  Sat Jul  9 17:11:39 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 9 Jul 2016 17:11:39 -0400
Subject: [MINC-users] direction cosines to xfm?
Message-ID: <CABEEk15tnv2wCitj+eGe36bFaSMyYMjYLmCmj8-Nnuk9yRGRBw@mail.gmail.com>

Hello,

I was wondering if anybody has something lying around that can convert the
direction cosines of a MINC volume into an explicit xfm file?

I assume that would be a mincinfo call to get starts and direction cosines,
then (with some math magic?) write that out as a .xfm. It's the magic bit
that I am hoping somebody may have figured out already :)

Thanks,

-- Alex

From zijdenbos at gmail.com  Sat Jul  9 23:21:54 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 9 Jul 2016 23:21:54 -0400
Subject: [MINC-users] direction cosines to xfm?
In-Reply-To: <CABEEk15tnv2wCitj+eGe36bFaSMyYMjYLmCmj8-Nnuk9yRGRBw@mail.gmail.com>
References: <CABEEk15tnv2wCitj+eGe36bFaSMyYMjYLmCmj8-Nnuk9yRGRBw@mail.gmail.com>
Message-ID: <CABEEk17fmBxe4wMiGGAs3ZvxhHkvuLu4H3sKyb6ftg6-we4+_g@mail.gmail.com>

... ok I believe I found it, in dircos_to_xfm, included in EZminc

Thanks, Vlad! :-)

On Sat, Jul 9, 2016 at 5:11 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hello,
>
> I was wondering if anybody has something lying around that can convert the
> direction cosines of a MINC volume into an explicit xfm file?
>
> I assume that would be a mincinfo call to get starts and direction
> cosines, then (with some math magic?) write that out as a .xfm. It's the
> magic bit that I am hoping somebody may have figured out already :)
>
> Thanks,
>
> -- Alex
>

From sorench at gmail.com  Mon Jul 11 11:47:38 2016
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 11 Jul 2016 08:47:38 -0700
Subject: [MINC-users] minc-toolkit-v2 libz issue
Message-ID: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>

Hi,
 I have a library resolution problem when building minc-toolkit-v2 on
ubuntu 16.04.
Cmake is set to NOT use the system libz, so I am puzzled that what seems to
be a libz function fails to resolve another libz function in the libz
provided by the package - what am I missing?
Thanks!
Soren

[ 24%] Linking C executable mnc2nii
../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function `znzopen':
znzlib.c:(.text+0x7d): undefined reference to `gzopen'
../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
`znzdopen':
znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
`Xznzclose':
znzlib.c:(.text+0x17d): undefined reference to `gzclose'
../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function `znzread':
znzlib.c:(.text+0x24c): undefined reference to `gzread'
.....

From vladimir.fonov at gmail.com  Mon Jul 11 11:57:02 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 11 Jul 2016 11:57:02 -0400
Subject: [MINC-users] minc-toolkit-v2 libz issue
In-Reply-To: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
References: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
Message-ID: <5783C1CE.4000707@gmail.com>

Hello,


are you using master or develop branch?

On 2016-07-11 11:47 AM, Soren Christensen wrote:
> Hi,
>   I have a library resolution problem when building minc-toolkit-v2 on
> ubuntu 16.04.
> Cmake is set to NOT use the system libz, so I am puzzled that what seems to
> be a libz function fails to resolve another libz function in the libz
> provided by the package - what am I missing?
> Thanks!
> Soren
>
> [ 24%] Linking C executable mnc2nii
> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function `znzopen':
> znzlib.c:(.text+0x7d): undefined reference to `gzopen'
> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
> `znzdopen':
> znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
> `Xznzclose':
> znzlib.c:(.text+0x17d): undefined reference to `gzclose'
> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function `znzread':
> znzlib.c:(.text+0x24c): undefined reference to `gzread'
> .....
> _______________________________________________
> 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  Mon Jul 11 12:09:32 2016
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 11 Jul 2016 09:09:32 -0700
Subject: [MINC-users] minc-toolkit-v2 libz issue
In-Reply-To: <5783C1CE.4000707@gmail.com>
References: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
	<5783C1CE.4000707@gmail.com>
Message-ID: <CAHfsrRaeCwZpvorMQVBSF-6MQs2Yc-6yjM3CcViUijagPFWinQ@mail.gmail.com>

Hi Vlad,
 Master branch

On Mon, Jul 11, 2016 at 8:57 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Hello,
>
>
> are you using master or develop branch?
>
>
> On 2016-07-11 11:47 AM, Soren Christensen wrote:
>
>> Hi,
>>   I have a library resolution problem when building minc-toolkit-v2 on
>> ubuntu 16.04.
>> Cmake is set to NOT use the system libz, so I am puzzled that what seems
>> to
>> be a libz function fails to resolve another libz function in the libz
>> provided by the package - what am I missing?
>> Thanks!
>> Soren
>>
>> [ 24%] Linking C executable mnc2nii
>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>> `znzopen':
>> znzlib.c:(.text+0x7d): undefined reference to `gzopen'
>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>> `znzdopen':
>> znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>> `Xznzclose':
>> znzlib.c:(.text+0x17d): undefined reference to `gzclose'
>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>> `znzread':
>> znzlib.c:(.text+0x24c): undefined reference to `gzread'
>> .....
>> _______________________________________________
>> 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 Jul 11 12:15:14 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 11 Jul 2016 12:15:14 -0400
Subject: [MINC-users] minc-toolkit-v2 libz issue
In-Reply-To: <CAHfsrRaeCwZpvorMQVBSF-6MQs2Yc-6yjM3CcViUijagPFWinQ@mail.gmail.com>
References: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
	<5783C1CE.4000707@gmail.com>
	<CAHfsrRaeCwZpvorMQVBSF-6MQs2Yc-6yjM3CcViUijagPFWinQ@mail.gmail.com>
Message-ID: <5783C612.8040004@gmail.com>

Try develop, i think i fixed this issue there

On 2016-07-11 12:09 PM, Soren Christensen wrote:
> Hi Vlad,
>   Master branch
>
> On Mon, Jul 11, 2016 at 8:57 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>> wrote:
>
>> Hello,
>>
>>
>> are you using master or develop branch?
>>
>>
>> On 2016-07-11 11:47 AM, Soren Christensen wrote:
>>
>>> Hi,
>>>    I have a library resolution problem when building minc-toolkit-v2 on
>>> ubuntu 16.04.
>>> Cmake is set to NOT use the system libz, so I am puzzled that what seems
>>> to
>>> be a libz function fails to resolve another libz function in the libz
>>> provided by the package - what am I missing?
>>> Thanks!
>>> Soren
>>>
>>> [ 24%] Linking C executable mnc2nii
>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>> `znzopen':
>>> znzlib.c:(.text+0x7d): undefined reference to `gzopen'
>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>> `znzdopen':
>>> znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>> `Xznzclose':
>>> znzlib.c:(.text+0x17d): undefined reference to `gzclose'
>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>> `znzread':
>>> znzlib.c:(.text+0x24c): undefined reference to `gzread'
>>> .....
>>> _______________________________________________
>>> 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 sorench at gmail.com  Mon Jul 11 17:25:49 2016
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 11 Jul 2016 14:25:49 -0700
Subject: [MINC-users] minc-toolkit-v2 libz issue
In-Reply-To: <5783C612.8040004@gmail.com>
References: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
	<5783C1CE.4000707@gmail.com>
	<CAHfsrRaeCwZpvorMQVBSF-6MQs2Yc-6yjM3CcViUijagPFWinQ@mail.gmail.com>
	<5783C612.8040004@gmail.com>
Message-ID: <CAHfsrRabgjC5OxBHE0gGvaj804OeFHEd1-vGcT3YkkR5Do-FSg@mail.gmail.com>

It seems to give the same result.
What is causing this - link order or something like that?

On Mon, Jul 11, 2016 at 9:15 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Try develop, i think i fixed this issue there
>
>
> On 2016-07-11 12:09 PM, Soren Christensen wrote:
>
>> Hi Vlad,
>>   Master branch
>>
>> On Mon, Jul 11, 2016 at 8:57 AM, Vladimir S. FONOV <
>> vladimir.fonov at gmail.com
>>
>>> wrote:
>>>
>>
>> Hello,
>>>
>>>
>>> are you using master or develop branch?
>>>
>>>
>>> On 2016-07-11 11:47 AM, Soren Christensen wrote:
>>>
>>> Hi,
>>>>    I have a library resolution problem when building minc-toolkit-v2 on
>>>> ubuntu 16.04.
>>>> Cmake is set to NOT use the system libz, so I am puzzled that what seems
>>>> to
>>>> be a libz function fails to resolve another libz function in the libz
>>>> provided by the package - what am I missing?
>>>> Thanks!
>>>> Soren
>>>>
>>>> [ 24%] Linking C executable mnc2nii
>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>> `znzopen':
>>>> znzlib.c:(.text+0x7d): undefined reference to `gzopen'
>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>> `znzdopen':
>>>> znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>> `Xznzclose':
>>>> znzlib.c:(.text+0x17d): undefined reference to `gzclose'
>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>> `znzread':
>>>> znzlib.c:(.text+0x24c): undefined reference to `gzread'
>>>> .....
>>>> _______________________________________________
>>>> 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 Jul 11 17:46:48 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 11 Jul 2016 17:46:48 -0400
Subject: [MINC-users] minc-toolkit-v2 libz issue
In-Reply-To: <CAHfsrRabgjC5OxBHE0gGvaj804OeFHEd1-vGcT3YkkR5Do-FSg@mail.gmail.com>
References: <CAHfsrRb98_X-5QYPjh3ytp+3v19p4=L6j98gFV3XgMmMV877Zg@mail.gmail.com>
	<5783C1CE.4000707@gmail.com>
	<CAHfsrRaeCwZpvorMQVBSF-6MQs2Yc-6yjM3CcViUijagPFWinQ@mail.gmail.com>
	<5783C612.8040004@gmail.com>
	<CAHfsrRabgjC5OxBHE0gGvaj804OeFHEd1-vGcT3YkkR5Do-FSg@mail.gmail.com>
Message-ID: <578413C8.9010009@gmail.com>

probably link order , gzopen is from Zlib and znzlib is from libnifti

On 2016-07-11 05:25 PM, Soren Christensen wrote:
> It seems to give the same result.
> What is causing this - link order or something like that?
>
> On Mon, Jul 11, 2016 at 9:15 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>> wrote:
>
>> Try develop, i think i fixed this issue there
>>
>>
>> On 2016-07-11 12:09 PM, Soren Christensen wrote:
>>
>>> Hi Vlad,
>>>    Master branch
>>>
>>> On Mon, Jul 11, 2016 at 8:57 AM, Vladimir S. FONOV <
>>> vladimir.fonov at gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>> Hello,
>>>>
>>>>
>>>> are you using master or develop branch?
>>>>
>>>>
>>>> On 2016-07-11 11:47 AM, Soren Christensen wrote:
>>>>
>>>> Hi,
>>>>>     I have a library resolution problem when building minc-toolkit-v2 on
>>>>> ubuntu 16.04.
>>>>> Cmake is set to NOT use the system libz, so I am puzzled that what seems
>>>>> to
>>>>> be a libz function fails to resolve another libz function in the libz
>>>>> provided by the package - what am I missing?
>>>>> Thanks!
>>>>> Soren
>>>>>
>>>>> [ 24%] Linking C executable mnc2nii
>>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>>> `znzopen':
>>>>> znzlib.c:(.text+0x7d): undefined reference to `gzopen'
>>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>>> `znzdopen':
>>>>> znzlib.c:(.text+0x11d): undefined reference to `gzdopen'
>>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>>> `Xznzclose':
>>>>> znzlib.c:(.text+0x17d): undefined reference to `gzclose'
>>>>> ../../external//usr/local/MNI/lib/libznz.a(znzlib.o): In function
>>>>> `znzread':
>>>>> znzlib.c:(.text+0x24c): undefined reference to `gzread'
>>>>> .....
>>>>> _______________________________________________
>>>>> 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 mishkind at gmail.com  Tue Jul 12 16:23:49 2016
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Tue, 12 Jul 2016 10:23:49 -1000
Subject: [MINC-users] minctracc glibc error detected
Message-ID: <CAB-GmL06_RrX2G+D1QY2Mz7UbF=puFu1T17K-MXJdjKEKh+E=Q@mail.gmail.com>

Aloha,

For reasons I won't get into here, I am using an older version of minctracc

mni-autoreg version 0.99.2
$ minctracc -version
The program <minctracc> was built from:
Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu) on
Mon May  8 23:16:34 EDT 2006

minc version 1.4
$ mincinfo -version
program: 1.4
libminc: 1.4
netcdf : 3.6.1 of May 11 2015 21:32:07 $


The problem is that *sometimes* I get core dumps, i.e., on some subjects
but not all. From what I can google from the error, I'm guessing it is an
array out of bounds issue, and I'm also going to guess this was fixed in a
later release of mni-autoreg or minc. Can anyone point me in the right
direction. I'm hoping that maybe I can apply a small patch to minctracc in
0.99.2, recompile it, and then still have a version of minctracc that
produces the same results as 0.99.2 in the cases where it doesn't fail.

Mahalo,
mishkin

Here is a sample command line:
minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
-transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
-clobber

Here is the default error/output:
*** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***

Here is the debugging output:
*** glibc detected *** minctracc: free(): invalid next size (normal):
0x08e9e560 ***
======= Backtrace: =========
/lib/libc.so.6(+0x70c91)[0x55657c91]
/lib/libc.so.6(+0x736f1)[0x5565a6f1]
minctracc[0x80a3ea8]
minctracc[0x80501af]
minctracc[0x8051461]
minctracc[0x8053e8c]
minctracc[0x804c06a]
/lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
minctracc[0x8049881]
======= Memory map: ========
08048000-080d5000 r-xp 00000000 00:13 52030078
minctracc
080d5000-080d8000 rw-p 0008d000 00:13 52030078
 minctracc
080d8000-080da000 rw-p 00000000 00:00 0
08e96000-08eee000 rw-p 00000000 00:00 0
 [heap]
55555000-55573000 r-xp 00000000 fd:01 18326
 /lib/ld-2.12.so
55573000-55574000 r--p 0001e000 fd:01 18326
 /lib/ld-2.12.so
55574000-55575000 rw-p 0001f000 fd:01 18326
 /lib/ld-2.12.so
55575000-55576000 r-xp 00000000 00:00 0
 [vdso]
55576000-55577000 rw-p 00000000 00:00 0
55577000-555ab000 r-xp 00000000 00:13 51884124
libnetcdf.so.3.6.1
555ab000-555ac000 rw-p 00034000 00:13 51884124
libnetcdf.so.3.6.1
555ac000-555af000 rw-p 00000000 00:00 0
555bd000-555e5000 r-xp 00000000 fd:01 15234
 /lib/libm-2.12.so
555e5000-555e6000 r--p 00027000 fd:01 15234
 /lib/libm-2.12.so
555e6000-555e7000 rw-p 00028000 fd:01 15234
 /lib/libm-2.12.so
555e7000-55778000 r-xp 00000000 fd:01 3460
/lib/libc-2.12.so
55778000-55779000 ---p 00191000 fd:01 3460
/lib/libc-2.12.so
55779000-5577b000 r--p 00191000 fd:01 3460
/lib/libc-2.12.so
5577b000-5577c000 rw-p 00193000 fd:01 3460
/lib/libc-2.12.so
5577c000-56e45000 rw-p 00000000 00:00 0
56e55000-56e72000 r-xp 00000000 fd:01 12959
 /lib/libgcc_s-4.4.7-20120601.so.1
56e72000-56e73000 rw-p 0001d000 fd:01 12959
 /lib/libgcc_s-4.4.7-20120601.so.1
56f00000-56f21000 rw-p 00000000 00:00 0
56f21000-57000000 ---p 00000000 00:00 0
ffbfd000-ffc13000 rw-p 00000000 00:00 0
 [stack]
Abort (core dumped)

From robert.d.vincent at mcgill.ca  Tue Jul 12 22:22:24 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Tue, 12 Jul 2016 22:22:24 -0400
Subject: [MINC-users] minctracc glibc error detected
In-Reply-To: <CAB-GmL06_RrX2G+D1QY2Mz7UbF=puFu1T17K-MXJdjKEKh+E=Q@mail.gmail.com>
References: <CAB-GmL06_RrX2G+D1QY2Mz7UbF=puFu1T17K-MXJdjKEKh+E=Q@mail.gmail.com>
Message-ID: <CAAd5DeT=0OrKHhqqF+XMQGUKK3T0xui6iM_wib=Yw-jN9=p_gw@mail.gmail.com>

Hi,

I can't be certain, but looking through the git history I see at least one
possibility:

https://github.com/BIC-MNI/mni_autoreg/issues/7

    -bert


On Tue, Jul 12, 2016 at 4:23 PM, Mishkin Derakhshan <mishkind at gmail.com>
wrote:

> Aloha,
>
> For reasons I won't get into here, I am using an older version of minctracc
>
> mni-autoreg version 0.99.2
> $ minctracc -version
> The program <minctracc> was built from:
> Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu) on
> Mon May  8 23:16:34 EDT 2006
>
> minc version 1.4
> $ mincinfo -version
> program: 1.4
> libminc: 1.4
> netcdf : 3.6.1 of May 11 2015 21:32:07 $
>
>
> The problem is that *sometimes* I get core dumps, i.e., on some subjects
> but not all. From what I can google from the error, I'm guessing it is an
> array out of bounds issue, and I'm also going to guess this was fixed in a
> later release of mni-autoreg or minc. Can anyone point me in the right
> direction. I'm hoping that maybe I can apply a small patch to minctracc in
> 0.99.2, recompile it, and then still have a version of minctracc that
> produces the same results as 0.99.2 in the cases where it doesn't fail.
>
> Mahalo,
> mishkin
>
> Here is a sample command line:
> minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
> -transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
> -clobber
>
> Here is the default error/output:
> *** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***
>
> Here is the debugging output:
> *** glibc detected *** minctracc: free(): invalid next size (normal):
> 0x08e9e560 ***
> ======= Backtrace: =========
> /lib/libc.so.6(+0x70c91)[0x55657c91]
> /lib/libc.so.6(+0x736f1)[0x5565a6f1]
> minctracc[0x80a3ea8]
> minctracc[0x80501af]
> minctracc[0x8051461]
> minctracc[0x8053e8c]
> minctracc[0x804c06a]
> /lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
> minctracc[0x8049881]
> ======= Memory map: ========
> 08048000-080d5000 r-xp 00000000 00:13 52030078
> minctracc
> 080d5000-080d8000 rw-p 0008d000 00:13 52030078
>  minctracc
> 080d8000-080da000 rw-p 00000000 00:00 0
> 08e96000-08eee000 rw-p 00000000 00:00 0
>  [heap]
> 55555000-55573000 r-xp 00000000 fd:01 18326
>  /lib/ld-2.12.so
> 55573000-55574000 r--p 0001e000 fd:01 18326
>  /lib/ld-2.12.so
> 55574000-55575000 rw-p 0001f000 fd:01 18326
>  /lib/ld-2.12.so
> 55575000-55576000 r-xp 00000000 00:00 0
>  [vdso]
> 55576000-55577000 rw-p 00000000 00:00 0
> 55577000-555ab000 r-xp 00000000 00:13 51884124
> libnetcdf.so.3.6.1
> 555ab000-555ac000 rw-p 00034000 00:13 51884124
> libnetcdf.so.3.6.1
> 555ac000-555af000 rw-p 00000000 00:00 0
> 555bd000-555e5000 r-xp 00000000 fd:01 15234
>  /lib/libm-2.12.so
> 555e5000-555e6000 r--p 00027000 fd:01 15234
>  /lib/libm-2.12.so
> 555e6000-555e7000 rw-p 00028000 fd:01 15234
>  /lib/libm-2.12.so
> 555e7000-55778000 r-xp 00000000 fd:01 3460
> /lib/libc-2.12.so
> 55778000-55779000 ---p 00191000 fd:01 3460
> /lib/libc-2.12.so
> 55779000-5577b000 r--p 00191000 fd:01 3460
> /lib/libc-2.12.so
> 5577b000-5577c000 rw-p 00193000 fd:01 3460
> /lib/libc-2.12.so
> 5577c000-56e45000 rw-p 00000000 00:00 0
> 56e55000-56e72000 r-xp 00000000 fd:01 12959
>  /lib/libgcc_s-4.4.7-20120601.so.1
> 56e72000-56e73000 rw-p 0001d000 fd:01 12959
>  /lib/libgcc_s-4.4.7-20120601.so.1
> 56f00000-56f21000 rw-p 00000000 00:00 0
> 56f21000-57000000 ---p 00000000 00:00 0
> ffbfd000-ffc13000 rw-p 00000000 00:00 0
>  [stack]
> Abort (core dumped)
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Wed Jul 13 01:17:42 2016
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Wed, 13 Jul 2016 01:17:42 -0400
Subject: [MINC-users] minctracc glibc error detected
In-Reply-To: <CAAd5DeT=0OrKHhqqF+XMQGUKK3T0xui6iM_wib=Yw-jN9=p_gw@mail.gmail.com>
References: <CAB-GmL06_RrX2G+D1QY2Mz7UbF=puFu1T17K-MXJdjKEKh+E=Q@mail.gmail.com>
	<CAAd5DeT=0OrKHhqqF+XMQGUKK3T0xui6iM_wib=Yw-jN9=p_gw@mail.gmail.com>
Message-ID: <5785CEF6.7010208@gmail.com>

No, that's not it - the example doesn't have long file names.

On 16-07-12 10:22 PM, Robert D. Vincent wrote:
> Hi,
>
> I can't be certain, but looking through the git history I see at least one
> possibility:
>
> https://github.com/BIC-MNI/mni_autoreg/issues/7
>
>      -bert
>
>
> On Tue, Jul 12, 2016 at 4:23 PM, Mishkin Derakhshan <mishkind at gmail.com>
> wrote:
>
>> Aloha,
>>
>> For reasons I won't get into here, I am using an older version of minctracc
>>
>> mni-autoreg version 0.99.2
>> $ minctracc -version
>> The program <minctracc> was built from:
>> Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu) on
>> Mon May  8 23:16:34 EDT 2006
>>
>> minc version 1.4
>> $ mincinfo -version
>> program: 1.4
>> libminc: 1.4
>> netcdf : 3.6.1 of May 11 2015 21:32:07 $
>>
>>
>> The problem is that *sometimes* I get core dumps, i.e., on some subjects
>> but not all. From what I can google from the error, I'm guessing it is an
>> array out of bounds issue, and I'm also going to guess this was fixed in a
>> later release of mni-autoreg or minc. Can anyone point me in the right
>> direction. I'm hoping that maybe I can apply a small patch to minctracc in
>> 0.99.2, recompile it, and then still have a version of minctracc that
>> produces the same results as 0.99.2 in the cases where it doesn't fail.
>>
>> Mahalo,
>> mishkin
>>
>> Here is a sample command line:
>> minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
>> -transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
>> -clobber
>>
>> Here is the default error/output:
>> *** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***
>>
>> Here is the debugging output:
>> *** glibc detected *** minctracc: free(): invalid next size (normal):
>> 0x08e9e560 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6(+0x70c91)[0x55657c91]
>> /lib/libc.so.6(+0x736f1)[0x5565a6f1]
>> minctracc[0x80a3ea8]
>> minctracc[0x80501af]
>> minctracc[0x8051461]
>> minctracc[0x8053e8c]
>> minctracc[0x804c06a]
>> /lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
>> minctracc[0x8049881]
>> ======= Memory map: ========
>> 08048000-080d5000 r-xp 00000000 00:13 52030078
>> minctracc
>> 080d5000-080d8000 rw-p 0008d000 00:13 52030078
>>   minctracc
>> 080d8000-080da000 rw-p 00000000 00:00 0
>> 08e96000-08eee000 rw-p 00000000 00:00 0
>>   [heap]
>> 55555000-55573000 r-xp 00000000 fd:01 18326
>>   /lib/ld-2.12.so
>> 55573000-55574000 r--p 0001e000 fd:01 18326
>>   /lib/ld-2.12.so
>> 55574000-55575000 rw-p 0001f000 fd:01 18326
>>   /lib/ld-2.12.so
>> 55575000-55576000 r-xp 00000000 00:00 0
>>   [vdso]
>> 55576000-55577000 rw-p 00000000 00:00 0
>> 55577000-555ab000 r-xp 00000000 00:13 51884124
>> libnetcdf.so.3.6.1
>> 555ab000-555ac000 rw-p 00034000 00:13 51884124
>> libnetcdf.so.3.6.1
>> 555ac000-555af000 rw-p 00000000 00:00 0
>> 555bd000-555e5000 r-xp 00000000 fd:01 15234
>>   /lib/libm-2.12.so
>> 555e5000-555e6000 r--p 00027000 fd:01 15234
>>   /lib/libm-2.12.so
>> 555e6000-555e7000 rw-p 00028000 fd:01 15234
>>   /lib/libm-2.12.so
>> 555e7000-55778000 r-xp 00000000 fd:01 3460
>> /lib/libc-2.12.so
>> 55778000-55779000 ---p 00191000 fd:01 3460
>> /lib/libc-2.12.so
>> 55779000-5577b000 r--p 00191000 fd:01 3460
>> /lib/libc-2.12.so
>> 5577b000-5577c000 rw-p 00193000 fd:01 3460
>> /lib/libc-2.12.so
>> 5577c000-56e45000 rw-p 00000000 00:00 0
>> 56e55000-56e72000 r-xp 00000000 fd:01 12959
>>   /lib/libgcc_s-4.4.7-20120601.so.1
>> 56e72000-56e73000 rw-p 0001d000 fd:01 12959
>>   /lib/libgcc_s-4.4.7-20120601.so.1
>> 56f00000-56f21000 rw-p 00000000 00:00 0
>> 56f21000-57000000 ---p 00000000 00:00 0
>> ffbfd000-ffc13000 rw-p 00000000 00:00 0
>>   [stack]
>> Abort (core dumped)
>> _______________________________________________
>> 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 mishkind at gmail.com  Wed Jul 13 16:02:36 2016
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Wed, 13 Jul 2016 10:02:36 -1000
Subject: [MINC-users] minctracc glibc error detected
In-Reply-To: <5785CEF6.7010208@gmail.com>
References: <CAB-GmL06_RrX2G+D1QY2Mz7UbF=puFu1T17K-MXJdjKEKh+E=Q@mail.gmail.com>
	<CAAd5DeT=0OrKHhqqF+XMQGUKK3T0xui6iM_wib=Yw-jN9=p_gw@mail.gmail.com>
	<5785CEF6.7010208@gmail.com>
Message-ID: <CAB-GmL2dvVQDzHW2MSzN+Qg6D4+atmP-TdP1qgncLg-2JbZC0w@mail.gmail.com>

Sorry, I had to redact some information from the filenames for privacy
reasons. But none of the filenames were over 256 chars.

The actual filenames were like this:
Source has 61 chars
target has 55
model_mask has 66
transformation has 69
measure has 67



On Tue, Jul 12, 2016 at 7:17 PM, Vladimir S. Fonov <vladimir.fonov at gmail.com
> wrote:

> No, that's not it - the example doesn't have long file names.
>
>
> On 16-07-12 10:22 PM, Robert D. Vincent wrote:
>
>> Hi,
>>
>> I can't be certain, but looking through the git history I see at least one
>> possibility:
>>
>> https://github.com/BIC-MNI/mni_autoreg/issues/7
>>
>>      -bert
>>
>>
>> On Tue, Jul 12, 2016 at 4:23 PM, Mishkin Derakhshan <mishkind at gmail.com>
>> wrote:
>>
>> Aloha,
>>>
>>> For reasons I won't get into here, I am using an older version of
>>> minctracc
>>>
>>> mni-autoreg version 0.99.2
>>> $ minctracc -version
>>> The program <minctracc> was built from:
>>> Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu)
>>> on
>>> Mon May  8 23:16:34 EDT 2006
>>>
>>> minc version 1.4
>>> $ mincinfo -version
>>> program: 1.4
>>> libminc: 1.4
>>> netcdf : 3.6.1 of May 11 2015 21:32:07 $
>>>
>>>
>>> The problem is that *sometimes* I get core dumps, i.e., on some subjects
>>> but not all. From what I can google from the error, I'm guessing it is an
>>> array out of bounds issue, and I'm also going to guess this was fixed in
>>> a
>>> later release of mni-autoreg or minc. Can anyone point me in the right
>>> direction. I'm hoping that maybe I can apply a small patch to minctracc
>>> in
>>> 0.99.2, recompile it, and then still have a version of minctracc that
>>> produces the same results as 0.99.2 in the cases where it doesn't fail.
>>>
>>> Mahalo,
>>> mishkin
>>>
>>> Here is a sample command line:
>>> minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
>>> -transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
>>> -clobber
>>>
>>> Here is the default error/output:
>>> *** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***
>>>
>>> Here is the debugging output:
>>> *** glibc detected *** minctracc: free(): invalid next size (normal):
>>> 0x08e9e560 ***
>>> ======= Backtrace: =========
>>> /lib/libc.so.6(+0x70c91)[0x55657c91]
>>> /lib/libc.so.6(+0x736f1)[0x5565a6f1]
>>> minctracc[0x80a3ea8]
>>> minctracc[0x80501af]
>>> minctracc[0x8051461]
>>> minctracc[0x8053e8c]
>>> minctracc[0x804c06a]
>>> /lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
>>> minctracc[0x8049881]
>>> ======= Memory map: ========
>>> 08048000-080d5000 r-xp 00000000 00:13 52030078
>>> minctracc
>>> 080d5000-080d8000 rw-p 0008d000 00:13 52030078
>>>   minctracc
>>> 080d8000-080da000 rw-p 00000000 00:00 0
>>> 08e96000-08eee000 rw-p 00000000 00:00 0
>>>   [heap]
>>> 55555000-55573000 r-xp 00000000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55573000-55574000 r--p 0001e000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55574000-55575000 rw-p 0001f000 fd:01 18326
>>>   /lib/ld-2.12.so
>>> 55575000-55576000 r-xp 00000000 00:00 0
>>>   [vdso]
>>> 55576000-55577000 rw-p 00000000 00:00 0
>>> 55577000-555ab000 r-xp 00000000 00:13 51884124
>>> libnetcdf.so.3.6.1
>>> 555ab000-555ac000 rw-p 00034000 00:13 51884124
>>> libnetcdf.so.3.6.1
>>> 555ac000-555af000 rw-p 00000000 00:00 0
>>> 555bd000-555e5000 r-xp 00000000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e5000-555e6000 r--p 00027000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e6000-555e7000 rw-p 00028000 fd:01 15234
>>>   /lib/libm-2.12.so
>>> 555e7000-55778000 r-xp 00000000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 55778000-55779000 ---p 00191000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 55779000-5577b000 r--p 00191000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 5577b000-5577c000 rw-p 00193000 fd:01 3460
>>> /lib/libc-2.12.so
>>> 5577c000-56e45000 rw-p 00000000 00:00 0
>>> 56e55000-56e72000 r-xp 00000000 fd:01 12959
>>>   /lib/libgcc_s-4.4.7-20120601.so.1
>>> 56e72000-56e73000 rw-p 0001d000 fd:01 12959
>>>   /lib/libgcc_s-4.4.7-20120601.so.1
>>> 56f00000-56f21000 rw-p 00000000 00:00 0
>>> 56f21000-57000000 ---p 00000000 00:00 0
>>> ffbfd000-ffc13000 rw-p 00000000 00:00 0
>>>   [stack]
>>> Abort (core dumped)
>>> _______________________________________________
>>> 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  Fri Jul 15 12:40:36 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Fri, 15 Jul 2016 12:40:36 -0400
Subject: [MINC-users] [Announcement] MINC-VM 1.0 Release
Message-ID: <CAFQOoOp4Gt1KRZ9CBn3sBnm4=oj2Dz+sT+=sASQw_jqY5CovPQ@mail.gmail.com>

Hi all,

After a recent thread on minc-users asking about a VM [1] and the resulting
offer of several options, I thought it might be useful to a have an
up-to-date ?standardized? VM with the MINC tools [2].

My goal was to automate the VM production process so that as new versions
of OSes and tools are released it won?t be a huge manual process to
re-create the VM. I found that packer <https://www.packer.io/> is a tool
ideal for spinning up a VM, provisioning it, and exporting it in an
automated manner.

So, this is my announcement of the 1.0 release of MINC-VM, a Lubuntu-Core
16.04 VirtualBox VM, containing:

   - minc-toolkit-v1 <https://github.com/BIC-MNI/minc-toolkit>
   - minc-toolkit-v2 <https://github.com/BIC-MNI/minc-toolkit-v2>
   - pyminc <https://github.com/Mouse-Imaging-Centre/pyminc>
   - minc-stuffs <https://github.com/Mouse-Imaging-Centre/minc-stuffs>
   - R <https://www.r-project.org/>
   - RStudio <https://www.rstudio.com/>
   - RMINC <https://github.com/Mouse-Imaging-Centre/RMINC>
   - brain-view2 <https://github.com/Mouse-Imaging-Centre/brain-view2>
   - pyezminc <https://github.com/BIC-MNI/pyezminc>
   -

   itksnap 3.4.0 with MINC support <https://github.com/vfonov/itksnap3>
   -

   mni.cortical.statistics
   <https://github.com/BIC-MNI/mni.cortical.statistics>

You can find the packer build scripts, download the pre-constructed VM, and
submit issues at:
https://github.com/cobralab/MINC-VM

HashiCorp <https://www.hashicorp.com/> has generously provided a cloud
building and hosting account, so the VM build rebuilds once-a-day to keep
up to date with Ubuntu?s mainline. It also rebuilds when any changes are
pushed on Github. All prior versions are maintained for download as well.

[1] http://www.bic.mni.mcgill.ca/pipermail/minc-users/2016-May/004400.html
[2] https://xkcd.com/927/


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

From gdevenyi at gmail.com  Fri Jul 15 11:06:40 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Fri, 15 Jul 2016 11:06:40 -0400
Subject: [MINC-users] [Announcement] MINC-VM 1.0 Release
Message-ID: <CAFQOoOrVQmeZggeSVPX9NLrFSi3xAVRA8zb9aMDYhRCu3uzkGQ@mail.gmail.com>

Hi all,

After a recent thread on minc-users asking about a VM [1] and the resulting
offer of several options, I thought it might be useful to a have an
up-to-date ?standardized? VM with the MINC tools [2].

My goal was to automate the VM production process so that as new versions
of OSes and tools are released it won?t be a huge manual process to
re-create the VM. I found that packer <https://www.packer.io/> is a tool
ideal for spinning up a VM, provisioning it, and exporting it in an
automated manner.

So, this is my announcement of the 1.0 release of MINC-VM, a Lubuntu-Core
16.04 VirtualBox VM, containing:

   - minc-toolkit-v1 <https://github.com/BIC-MNI/minc-toolkit>
   - minc-toolkit-v2 <https://github.com/BIC-MNI/minc-toolkit-v2>
   - pyminc <https://github.com/Mouse-Imaging-Centre/pyminc>
   - minc-stuffs <https://github.com/Mouse-Imaging-Centre/minc-stuffs>
   - R <https://www.r-project.org/>
   - RStudio <https://www.rstudio.com>
   - RMINC <https://github.com/Mouse-Imaging-Centre/RMINC>
   - brain-view2 <https://github.com/Mouse-Imaging-Centre/brain-view2>
   - pyezminc <https://github.com/BIC-MNI/pyezminc>
   -

   itksnap 3.4.0 with MINC support <https://github.com/vfonov/itksnap3>
   -

   mni.cortical.statistics
   <https://github.com/BIC-MNI/mni.cortical.statistics>

You can find the packer build scripts, download the pre-constructed VM, and
submit issues at:
https://github.com/cobralab/MINC-VM

HashiCorp <https://www.hashicorp.com> has generously provided a cloud
building and hosting account, so the VM build rebuilds once-a-day to keep
up to date with Ubuntu?s mainline. It also rebuilds when any changes are
pushed on Github. All prior versions are maintained for download as well.

[1] http://www.bic.mni.mcgill.ca/pipermail/minc-users/2016-May/004400.html
[2] https://xkcd.com/927/

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

From zijdenbos at gmail.com  Wed Jul 20 00:13:11 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 20 Jul 2016 00:13:11 -0400
Subject: [MINC-users] mincreshape -normalize -fillvalue
Message-ID: <CABEEk179Y6YeCS_tXJ0JA8-uGJjOaS52PV5v+bxk30cqC0fyeQ@mail.gmail.com>

Hello all,

The -normalize option ("Normalize images to real minimum and maximum for
the entire input file") appears to disregard the fill value (if provided).
For example, if volume in.mnc has a range [5,100], this call:

mincreshape [-start ... ] -normalize -fillvalue 0 in.mnc out.mnc

actually fills with 5, not 0. I would consider that a bug, and say that
-normalize should include any out-of-current-range fill values in the final
range of the volume. Or?

On a related note: it's never been clear to me what the difference between
-pixfillvalue and -fillvalue is (and it's hardly clear from the man page).
Is that simply voxel value vs real value?

Thanks,

-- A

From trisanna.sprung-much at mail.mcgill.ca  Thu Jul 21 15:06:54 2016
From: trisanna.sprung-much at mail.mcgill.ca (Trisanna Sprung-Much)
Date: Thu, 21 Jul 2016 15:06:54 -0400
Subject: [MINC-users] nii2mnc
Message-ID: <CAG+ToRt4OYfRSFR+nYOqLGStd+NYpLXzZ691KQpWDhB24pEVXg@mail.gmail.com>

Hello

I recently tried to use nii2mnc on some ex-vivo scans and the command seems
to fail. Any ideas as to why? I think it has to do with the format of my
nifti file?

many thanks

Trisanna

nii2mnc: Convert NIfTI-1 files to MINC format
usage: nii2mnc [options] filename.nii [filename.mnc]
 nii2mnc Merv_7T.nii Merv_7T.mnc
<nifti_image
  nifti_type = 'NIFTI-1+'
  header_filename = 'Merv_7T.nii'
  image_filename = 'Merv_7T.nii'
  image_offset = '352'
  ndim = '3'
  nx = '280'
  ny = '280'
  nz = '80'
  dx = '0.428571'
  dy = '0.428571'
  dz = '1.5'
  datatype = '4'
  datatype_name = 'INT16'
  nvox = '6272000'
  nbyper = '2'
  byteorder = 'LSB_FIRST'
  scl_slope = '1'
  scl_inter = '0'
  xyz_units = '2'
  xyz_units_name = 'mm'
  time_units = '8'
  time_units_name = 's'
  descrip = 'FSL5.0'
  num_ext = '0'
/>
Segmentation fault (core dumped)

From vladimir.fonov at gmail.com  Thu Jul 21 17:03:11 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 21 Jul 2016 17:03:11 -0400
Subject: [MINC-users] nii2mnc
In-Reply-To: <CAG+ToRt4OYfRSFR+nYOqLGStd+NYpLXzZ691KQpWDhB24pEVXg@mail.gmail.com>
References: <CAG+ToRt4OYfRSFR+nYOqLGStd+NYpLXzZ691KQpWDhB24pEVXg@mail.gmail.com>
Message-ID: <4c14f33c-5ee6-0dc9-c744-18b65b51a5a8@gmail.com>

Hello,

it could fail for many reasons....
You can try itk_convert - see if it helps.

On 2016-07-21 03:06 PM, Trisanna Sprung-Much wrote:
> Hello
>
> I recently tried to use nii2mnc on some ex-vivo scans and the command seems
> to fail. Any ideas as to why? I think it has to do with the format of my
> nifti file?
>
> many thanks
>
> Trisanna
>
> nii2mnc: Convert NIfTI-1 files to MINC format
> usage: nii2mnc [options] filename.nii [filename.mnc]
>  nii2mnc Merv_7T.nii Merv_7T.mnc
> <nifti_image
>   nifti_type = 'NIFTI-1+'
>   header_filename = 'Merv_7T.nii'
>   image_filename = 'Merv_7T.nii'
>   image_offset = '352'
>   ndim = '3'
>   nx = '280'
>   ny = '280'
>   nz = '80'
>   dx = '0.428571'
>   dy = '0.428571'
>   dz = '1.5'
>   datatype = '4'
>   datatype_name = 'INT16'
>   nvox = '6272000'
>   nbyper = '2'
>   byteorder = 'LSB_FIRST'
>   scl_slope = '1'
>   scl_inter = '0'
>   xyz_units = '2'
>   xyz_units_name = 'mm'
>   time_units = '8'
>   time_units_name = 's'
>   descrip = 'FSL5.0'
>   num_ext = '0'
> />
> Segmentation fault (core dumped)
> _______________________________________________
> 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 a.janke at gmail.com  Thu Jul 21 23:26:19 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Jul 2016 13:26:19 +1000
Subject: [MINC-users] RGB volumes and register
Message-ID: <CAG0CB22hH1=opsjpL9mfE0PHWCiHWbmXYMMOW5x2at57OW7ycA@mail.gmail.com>

Probably for Bert,

Can anyone comment on how the current version of register in
minc-toolkit-v2 determines if a volume is RGB or not? It doens't seem
to be based upon dimension order as per previous versions.

This bit of old Dave McDonald code would insinuate that the volume has
to be an unsigned long?

   https://github.com/BIC-MNI/libminc/blob/develop/volume_io/Volumes/volumes.c#L568

Which is called deep within register:

   https://github.com/BIC-MNI/Register/search?utf8=%E2%9C%93&q=is_an_rgb_volume

?

So, the question remains, what dimension order, dimensions and
datatype should I use? Previously this was
vector_dimension,zspace,yspace,xspace + unsigned byte (0-255).

ta


a

From robert.d.vincent at mcgill.ca  Fri Jul 22 08:31:22 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Fri, 22 Jul 2016 08:31:22 -0400
Subject: [MINC-users] RGB volumes and register
In-Reply-To: <CAG0CB22hH1=opsjpL9mfE0PHWCiHWbmXYMMOW5x2at57OW7ycA@mail.gmail.com>
References: <CAG0CB22hH1=opsjpL9mfE0PHWCiHWbmXYMMOW5x2at57OW7ycA@mail.gmail.com>
Message-ID: <CAAd5DeSCJ1CN9o7sU2ZJ3cnFhtVc62QeD2HLumuesQCcaWqAWQ@mail.gmail.com>

Hi,

I accidentally disabled the RGB volume handling in volume_io a while ago,
then fixed it when it was reported. The current develop branch should work
as always.

See
https://github.com/BIC-MNI/libminc/commit/a1839e0d717f38e4bf1839a35a151796935d3b03

The actual test for RGB volumes starts at line 175 of input_mnc.c in the
current develop branch. The vector_dimension needs to be the final
dimension in the file and should be of length 3, generally. I don't think
the voxel type matters.

    -bert

On Thu, Jul 21, 2016 at 11:26 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Probably for Bert,
>
> Can anyone comment on how the current version of register in
> minc-toolkit-v2 determines if a volume is RGB or not? It doens't seem
> to be based upon dimension order as per previous versions.
>
> This bit of old Dave McDonald code would insinuate that the volume has
> to be an unsigned long?
>
>
> https://github.com/BIC-MNI/libminc/blob/develop/volume_io/Volumes/volumes.c#L568
>
> Which is called deep within register:
>
>
> https://github.com/BIC-MNI/Register/search?utf8=%E2%9C%93&q=is_an_rgb_volume
>
> ?
>
> So, the question remains, what dimension order, dimensions and
> datatype should I use? Previously this was
> vector_dimension,zspace,yspace,xspace + unsigned byte (0-255).
>
> ta
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From robert.d.vincent at mcgill.ca  Fri Jul 22 08:35:15 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Fri, 22 Jul 2016 08:35:15 -0400
Subject: [MINC-users] nii2mnc
In-Reply-To: <4c14f33c-5ee6-0dc9-c744-18b65b51a5a8@gmail.com>
References: <CAG+ToRt4OYfRSFR+nYOqLGStd+NYpLXzZ691KQpWDhB24pEVXg@mail.gmail.com>
	<4c14f33c-5ee6-0dc9-c744-18b65b51a5a8@gmail.com>
Message-ID: <CAAd5DeTc4bRAUGgzkeaSPF3xuv+pRXpf=P6St-Kbp4PQt51ypw@mail.gmail.com>

Hi Trisanna,

It looks like your file does not contain a specification of a spatial
transform from voxel to world space - the code to handle this in nii2mnc
was broken a while back. It's fixed now, but I don't think that version has
been officially released yet.

    -bert

On Thu, Jul 21, 2016 at 5:03 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Hello,
>
> it could fail for many reasons....
> You can try itk_convert - see if it helps.
>
>
> On 2016-07-21 03:06 PM, Trisanna Sprung-Much wrote:
>
>> Hello
>>
>> I recently tried to use nii2mnc on some ex-vivo scans and the command
>> seems
>> to fail. Any ideas as to why? I think it has to do with the format of my
>> nifti file?
>>
>> many thanks
>>
>> Trisanna
>>
>> nii2mnc: Convert NIfTI-1 files to MINC format
>> usage: nii2mnc [options] filename.nii [filename.mnc]
>>  nii2mnc Merv_7T.nii Merv_7T.mnc
>> <nifti_image
>>   nifti_type = 'NIFTI-1+'
>>   header_filename = 'Merv_7T.nii'
>>   image_filename = 'Merv_7T.nii'
>>   image_offset = '352'
>>   ndim = '3'
>>   nx = '280'
>>   ny = '280'
>>   nz = '80'
>>   dx = '0.428571'
>>   dy = '0.428571'
>>   dz = '1.5'
>>   datatype = '4'
>>   datatype_name = 'INT16'
>>   nvox = '6272000'
>>   nbyper = '2'
>>   byteorder = 'LSB_FIRST'
>>   scl_slope = '1'
>>   scl_inter = '0'
>>   xyz_units = '2'
>>   xyz_units_name = 'mm'
>>   time_units = '8'
>>   time_units_name = 's'
>>   descrip = 'FSL5.0'
>>   num_ext = '0'
>> />
>> Segmentation fault (core dumped)
>> _______________________________________________
>> 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 ptcougopinto at gmail.com  Fri Jul 22 09:16:38 2016
From: ptcougopinto at gmail.com (Pedro)
Date: Fri, 22 Jul 2016 10:16:38 -0300
Subject: [MINC-users] nu_corrrect: bias files image
Message-ID: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>

Hi

Is there a way to get an image of bias filed from nu_correct (or related scripts)?

Pedro




From vladimir.fonov at gmail.com  Fri Jul 22 09:20:13 2016
From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com)
Date: Fri, 22 Jul 2016 09:20:13 -0400
Subject: [MINC-users] nu_corrrect: bias files image
In-Reply-To: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
References: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
Message-ID: <0315D245-0D9C-4486-B732-4E7FF1B6A99E@gmail.com>

Hello,


nu_estimate will produce .imp file that can be converted to the bias field using nu_evaluate.

nu_correct is actually a wrapper around these two programs. 

> On Jul 22, 2016, at 09:16, Pedro <ptcougopinto at gmail.com> wrote:
> 
> Hi
> 
> Is there a way to get an image of bias filed from nu_correct (or related scripts)?
> 
> Pedro
> 
> 
> 
> _______________________________________________
> 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  Fri Jul 22 09:26:23 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 22 Jul 2016 09:26:23 -0400
Subject: [MINC-users] nu_corrrect: bias files image
In-Reply-To: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
References: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
Message-ID: <CABEEk16xHMKxHWYv2r24NHFskxfakbdJc=MmbdVNzeSrYdfpdA@mail.gmail.com>

Hi Pedro,

Yes - nu_correct is just a wrapper around nu_estimate* and nu_evaluate.
If you call nu_correct with -mapping_dir, you can then use nu_evaluate to
convert the .imp file generated in that dir, into a volume.

-- A

On Fri, Jul 22, 2016 at 9:16 AM, Pedro <ptcougopinto at gmail.com> wrote:

> Hi
>
> Is there a way to get an image of bias filed from nu_correct (or related
> scripts)?
>
> Pedro
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From ptcougopinto at gmail.com  Fri Jul 22 09:34:19 2016
From: ptcougopinto at gmail.com (Pedro)
Date: Fri, 22 Jul 2016 10:34:19 -0300
Subject: [MINC-users] nu_corrrect: bias files image
In-Reply-To: <CABEEk16xHMKxHWYv2r24NHFskxfakbdJc=MmbdVNzeSrYdfpdA@mail.gmail.com>
References: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
	<CABEEk16xHMKxHWYv2r24NHFskxfakbdJc=MmbdVNzeSrYdfpdA@mail.gmail.com>
Message-ID: <323EA7AE-98AD-41EC-8030-95CAD567B70E@gmail.com>

Got it. It would be interesting to have the -field option (as for nu_evaluate) for nu_correct.

Thanks!
Pedro
> Em 22 de jul de 2016, ?(s) 10:26, Alex Zijdenbos <zijdenbos at gmail.com> escreveu:
> 
> Hi Pedro,
> 
> Yes - nu_correct is just a wrapper around nu_estimate* and nu_evaluate.
> If you call nu_correct with -mapping_dir, you can then use nu_evaluate to
> convert the .imp file generated in that dir, into a volume.
> 
> -- A
> 
> On Fri, Jul 22, 2016 at 9:16 AM, Pedro <ptcougopinto at gmail.com> wrote:
> 
>> Hi
>> 
>> Is there a way to get an image of bias filed from nu_correct (or related
>> scripts)?
>> 
>> Pedro
>> 
>> 
>> 
>> _______________________________________________
>> 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 john.sled at utoronto.ca  Fri Jul 22 09:42:37 2016
From: john.sled at utoronto.ca (John G. Sled)
Date: Fri, 22 Jul 2016 09:42:37 -0400
Subject: [MINC-users] nu_corrrect: bias files image
In-Reply-To: <323EA7AE-98AD-41EC-8030-95CAD567B70E@gmail.com>
References: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
	<CABEEk16xHMKxHWYv2r24NHFskxfakbdJc=MmbdVNzeSrYdfpdA@mail.gmail.com>
	<323EA7AE-98AD-41EC-8030-95CAD567B70E@gmail.com>
Message-ID: <0C8453E2-2FE0-4F49-B62D-FE3223F89671@utoronto.ca>

Hi Pedro,

There is a script called imp2field that creates a minc volume based on the field in the .imp file.

cheers,

John


> On Jul 22, 2016, at 9:34 AM, Pedro <ptcougopinto at gmail.com> wrote:
> 
> Got it. It would be interesting to have the -field option (as for nu_evaluate) for nu_correct.
> 
> Thanks!
> Pedro
>> Em 22 de jul de 2016, ?(s) 10:26, Alex Zijdenbos <zijdenbos at gmail.com> escreveu:
>> 
>> Hi Pedro,
>> 
>> Yes - nu_correct is just a wrapper around nu_estimate* and nu_evaluate.
>> If you call nu_correct with -mapping_dir, you can then use nu_evaluate to
>> convert the .imp file generated in that dir, into a volume.
>> 
>> -- A
>> 
>> On Fri, Jul 22, 2016 at 9:16 AM, Pedro <ptcougopinto at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> Is there a way to get an image of bias filed from nu_correct (or related
>>> scripts)?
>>> 
>>> Pedro
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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  Fri Jul 22 09:40:13 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Fri, 22 Jul 2016 09:40:13 -0400
Subject: [MINC-users] nu_corrrect: bias files image
In-Reply-To: <323EA7AE-98AD-41EC-8030-95CAD567B70E@gmail.com>
References: <A43964AC-824C-4DB3-B1BF-50EB1865DABE@gmail.com>
	<CABEEk16xHMKxHWYv2r24NHFskxfakbdJc=MmbdVNzeSrYdfpdA@mail.gmail.com>
	<323EA7AE-98AD-41EC-8030-95CAD567B70E@gmail.com>
Message-ID: <CAFQOoOpLcB0NyakkO_vdDhtVw=kznwOh42DzOC7hLJ=2YuwNkg@mail.gmail.com>

N3BiasFieldCorrection from ANTs can save a bias field as part of its output
as well.

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

On Fri, Jul 22, 2016 at 9:34 AM, Pedro <ptcougopinto at gmail.com> wrote:

> Got it. It would be interesting to have the -field option (as for
> nu_evaluate) for nu_correct.
>
> Thanks!
> Pedro
> > Em 22 de jul de 2016, ?(s) 10:26, Alex Zijdenbos <zijdenbos at gmail.com>
> escreveu:
> >
> > Hi Pedro,
> >
> > Yes - nu_correct is just a wrapper around nu_estimate* and nu_evaluate.
> > If you call nu_correct with -mapping_dir, you can then use nu_evaluate to
> > convert the .imp file generated in that dir, into a volume.
> >
> > -- A
> >
> > On Fri, Jul 22, 2016 at 9:16 AM, Pedro <ptcougopinto at gmail.com> wrote:
> >
> >> Hi
> >>
> >> Is there a way to get an image of bias filed from nu_correct (or related
> >> scripts)?
> >>
> >> Pedro
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 trisanna.sprung-much at mail.mcgill.ca  Fri Jul 22 10:41:35 2016
From: trisanna.sprung-much at mail.mcgill.ca (Trisanna Sprung-Much)
Date: Fri, 22 Jul 2016 10:41:35 -0400
Subject: [MINC-users] nii2mnc
In-Reply-To: <22828_1469190991_5792134F_22828_160_1_CAAd5DeTc4bRAUGgzkeaSPF3xuv+pRXpf=P6St-Kbp4PQt51ypw@mail.gmail.com>
References: <CAG+ToRt4OYfRSFR+nYOqLGStd+NYpLXzZ691KQpWDhB24pEVXg@mail.gmail.com>
	<4c14f33c-5ee6-0dc9-c744-18b65b51a5a8@gmail.com>
	<22828_1469190991_5792134F_22828_160_1_CAAd5DeTc4bRAUGgzkeaSPF3xuv+pRXpf=P6St-Kbp4PQt51ypw@mail.gmail.com>
Message-ID: <CAG+ToRugt18uHiBKXy4Pe2R+_5YF-xLbcWxTC7-UyNjJvL3Miw@mail.gmail.com>

thanks, Robert. Will see if I can get the original dicoms instead.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jul 22, 2016 at 8:35 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Trisanna,
>
> It looks like your file does not contain a specification of a spatial
> transform from voxel to world space - the code to handle this in nii2mnc
> was broken a while back. It's fixed now, but I don't think that version has
> been officially released yet.
>
>     -bert
>
> On Thu, Jul 21, 2016 at 5:03 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com
> > wrote:
>
> > Hello,
> >
> > it could fail for many reasons....
> > You can try itk_convert - see if it helps.
> >
> >
> > On 2016-07-21 03:06 PM, Trisanna Sprung-Much wrote:
> >
> >> Hello
> >>
> >> I recently tried to use nii2mnc on some ex-vivo scans and the command
> >> seems
> >> to fail. Any ideas as to why? I think it has to do with the format of my
> >> nifti file?
> >>
> >> many thanks
> >>
> >> Trisanna
> >>
> >> nii2mnc: Convert NIfTI-1 files to MINC format
> >> usage: nii2mnc [options] filename.nii [filename.mnc]
> >>  nii2mnc Merv_7T.nii Merv_7T.mnc
> >> <nifti_image
> >>   nifti_type = 'NIFTI-1+'
> >>   header_filename = 'Merv_7T.nii'
> >>   image_filename = 'Merv_7T.nii'
> >>   image_offset = '352'
> >>   ndim = '3'
> >>   nx = '280'
> >>   ny = '280'
> >>   nz = '80'
> >>   dx = '0.428571'
> >>   dy = '0.428571'
> >>   dz = '1.5'
> >>   datatype = '4'
> >>   datatype_name = 'INT16'
> >>   nvox = '6272000'
> >>   nbyper = '2'
> >>   byteorder = 'LSB_FIRST'
> >>   scl_slope = '1'
> >>   scl_inter = '0'
> >>   xyz_units = '2'
> >>   xyz_units_name = 'mm'
> >>   time_units = '8'
> >>   time_units_name = 's'
> >>   descrip = 'FSL5.0'
> >>   num_ext = '0'
> >> />
> >> Segmentation fault (core dumped)
> >> _______________________________________________
> >> 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
>

From vladimir.fonov at gmail.com  Fri Jul 22 13:49:46 2016
From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com)
Date: Fri, 22 Jul 2016 13:49:46 -0400
Subject: [MINC-users] Updates on MINC wiki books
Message-ID: <F8728E10-9A83-4142-9F84-80405C94E42E@gmail.com>

Hello Everybody,

I have started updating https://en.wikibooks.org/wiki/MINC to reflect current state of affairs. In particular I have created a page describing current users and developers of MINC and MINC-based tools. This list is currently incomplete, could you take a look at https://en.wikibooks.org/wiki/MINC/MincWorld and send me suggestions (or  create an account on wikibooks and links yourself). 

---
Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info





From a.janke at gmail.com  Sat Jul 23 09:27:17 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 23 Jul 2016 23:27:17 +1000
Subject: [MINC-users] RGB volumes and register
In-Reply-To: <CAAd5DeSCJ1CN9o7sU2ZJ3cnFhtVc62QeD2HLumuesQCcaWqAWQ@mail.gmail.com>
References: <CAG0CB22hH1=opsjpL9mfE0PHWCiHWbmXYMMOW5x2at57OW7ycA@mail.gmail.com>
	<CAAd5DeSCJ1CN9o7sU2ZJ3cnFhtVc62QeD2HLumuesQCcaWqAWQ@mail.gmail.com>
Message-ID: <CAG0CB22m8oA1dSvBQ9vjUME22++DNeUrbHsgMZ9e6=diYCi-nA@mail.gmail.com>

Thanks,

I'll take a crack at building it from source.


a


On 22 July 2016 at 22:31, Robert D. Vincent <robert.d.vincent at mcgill.ca> wrote:
> Hi,
>
> I accidentally disabled the RGB volume handling in volume_io a while ago,
> then fixed it when it was reported. The current develop branch should work
> as always.
>
> See
> https://github.com/BIC-MNI/libminc/commit/a1839e0d717f38e4bf1839a35a151796935d3b03
>
> The actual test for RGB volumes starts at line 175 of input_mnc.c in the
> current develop branch. The vector_dimension needs to be the final
> dimension in the file and should be of length 3, generally. I don't think
> the voxel type matters.
>
>     -bert
>
> On Thu, Jul 21, 2016 at 11:26 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Probably for Bert,
>>
>> Can anyone comment on how the current version of register in
>> minc-toolkit-v2 determines if a volume is RGB or not? It doens't seem
>> to be based upon dimension order as per previous versions.
>>
>> This bit of old Dave McDonald code would insinuate that the volume has
>> to be an unsigned long?
>>
>>
>> https://github.com/BIC-MNI/libminc/blob/develop/volume_io/Volumes/volumes.c#L568
>>
>> Which is called deep within register:
>>
>>
>> https://github.com/BIC-MNI/Register/search?utf8=%E2%9C%93&q=is_an_rgb_volume
>>
>> ?
>>
>> So, the question remains, what dimension order, dimensions and
>> datatype should I use? Previously this was
>> vector_dimension,zspace,yspace,xspace + unsigned byte (0-255).
>>
>> ta
>>
>>
>> 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 andrew at biospective.com  Mon Jul 25 14:00:32 2016
From: andrew at biospective.com (Andrew Wood)
Date: Mon, 25 Jul 2016 14:00:32 -0400
Subject: [MINC-users] Minc Flood Fill
Message-ID: <CABApf9HOHicHtvwYwQodoE5WFnzjPJW887hU7GoG2-pFHHdG+Q@mail.gmail.com>

Hi all,

I'm wondering if a minc tool exists that can do a flood fill operation. It
would take:
  1) an image
  2) a label volume, defining seed regions
  3) a threshold, defining the "aggressiveness" of the fill

Display can do it ("set threshold" and "label fill" in the Segmenting
menu), but of course requires a human user; I was hoping for a tool that
could be used in an automated pipeline.

Thanks,
Andrew

From daniel at biospective.com  Tue Jul 26 13:05:35 2016
From: daniel at biospective.com (Daniel Marchand)
Date: Tue, 26 Jul 2016 13:05:35 -0400
Subject: [MINC-users] dcm2mnc error regarding PatientAge
Message-ID: <CALZEBsYNOnpxS-opkovO6mJFu1Xf-a1BeHjHNYbdPxNPLdz0Uw@mail.gmail.com>

Hi,

I'm having trouble converting a dicom file including the line:
(0010,1010) AS [0000]                                   #   4, 1 PatientAge

which throws the error:
Age units (0000) unknown

It seems that the cause of the error is
inside of conversion/dcm2mnc/minc_file.c :

    if (strlen(general_info->patient.age) > 0) {
        string_t temp;
        int i;
        double age;

        strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
        while (temp[i] != 0 && !isdigit(temp[i]))
          i++;
        if (temp[i] == 0) {
          fprintf(stderr, "ERROR: Age was not numeric!!\n");
          exit(-1);
        }
        age = atof(&temp[i]);
        while (temp[i] != 0 && isdigit(temp[i]))
          i++;
        if (temp[i] == 'M')     /* age is in months */
          age /= 12.0;
        else if (temp[i] == 'W')   /* age is in weeks */
          age /= 52.0;
        else if (temp[i] == 'D')   /* age is in days */
          age /= 365.0;
        else if (temp[i] != 'Y') { /* age is in years */
          fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
          exit(-1);
        }
        miattputdbl(mincid, varid, MIage, age);

I would appear that perhaps a new option could be added where
dcm2mnc doesn't crash if the age is written as [0000]?

Best,

Daniel

From thomas.funck at mail.mcgill.ca  Tue Jul 26 14:36:14 2016
From: thomas.funck at mail.mcgill.ca (Thomas Funck, Mr)
Date: Tue, 26 Jul 2016 18:36:14 +0000
Subject: [MINC-users] Problem with ZLIB when compiling minc-toolkit-v2
Message-ID: <BN3PR03MB1445BC1E1A497B51E9AB82E1A60E0@BN3PR03MB1445.namprd03.prod.outlook.com>

Hi,

I'm trying to compile minc-toolkit-v2, but ran into the following problem. I'm trying to compile on Ubuntu 16.04.1 LTS and with USE_SYSTEM_ZLIB=OFF. I also tried minc-toolkit but ran into the same error.

Thanks for any help,

Thomas

Scanning dependencies of target nii2mnc
[ 23%] Building C object minctools/conversion/CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
[ 23%] Linking C executable nii2mnc
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzopen':
znzlib.c:(.text+0x4a): undefined reference to `gzopen'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzdopen':
znzlib.c:(.text+0x102): undefined reference to `gzdopen'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `Xznzclose':
znzlib.c:(.text+0x166): undefined reference to `gzclose'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzread':
znzlib.c:(.text+0x220): undefined reference to `gzread'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzwrite':
znzlib.c:(.text+0x320): undefined reference to `gzwrite'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzseek':
znzlib.c:(.text+0x3db): undefined reference to `gzseek'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzrewind':
znzlib.c:(.text+0x447): undefined reference to `gzseek'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znztell':
znzlib.c:(.text+0x4a3): undefined reference to `gztell'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputs':
znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgets':
znzlib.c:(.text+0x55b): undefined reference to `gzgets'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzflush':
znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzeof':
znzlib.c:(.text+0x623): undefined reference to `gzeof'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputc':
znzlib.c:(.text+0x677): undefined reference to `gzputc'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgetc':
znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzprintf':
znzlib.c:(.text+0x798): undefined reference to `gzprintf'
collect2: error: ld returned 1 exit status
minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for target 'minctools/conversion/nii2mnc' failed
make[2]: *** [minctools/conversion/nii2mnc] Error 1
CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all' failed
make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2


From vladimir.fonov at gmail.com  Tue Jul 26 14:43:17 2016
From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com)
Date: Tue, 26 Jul 2016 14:43:17 -0400
Subject: [MINC-users] Problem with ZLIB when compiling minc-toolkit-v2
In-Reply-To: <BN3PR03MB1445BC1E1A497B51E9AB82E1A60E0@BN3PR03MB1445.namprd03.prod.outlook.com>
References: <BN3PR03MB1445BC1E1A497B51E9AB82E1A60E0@BN3PR03MB1445.namprd03.prod.outlook.com>
Message-ID: <64C52D64-4ED0-4241-A956-8952D5B37DF9@gmail.com>

Can you try running ?make ZLIB? first , and then ?make nii2mnc? ?


> On Jul 26, 2016, at 14:36, Thomas Funck, Mr <thomas.funck at mail.mcgill.ca> wrote:
> 
> Hi,
> 
> I'm trying to compile minc-toolkit-v2, but ran into the following problem. I'm trying to compile on Ubuntu 16.04.1 LTS and with USE_SYSTEM_ZLIB=OFF. I also tried minc-toolkit but ran into the same error.
> 
> Thanks for any help,
> 
> Thomas
> 
> Scanning dependencies of target nii2mnc
> [ 23%] Building C object minctools/conversion/CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
> [ 23%] Linking C executable nii2mnc
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzopen':
> znzlib.c:(.text+0x4a): undefined reference to `gzopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzdopen':
> znzlib.c:(.text+0x102): undefined reference to `gzdopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `Xznzclose':
> znzlib.c:(.text+0x166): undefined reference to `gzclose'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzread':
> znzlib.c:(.text+0x220): undefined reference to `gzread'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzwrite':
> znzlib.c:(.text+0x320): undefined reference to `gzwrite'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzseek':
> znzlib.c:(.text+0x3db): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzrewind':
> znzlib.c:(.text+0x447): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znztell':
> znzlib.c:(.text+0x4a3): undefined reference to `gztell'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputs':
> znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgets':
> znzlib.c:(.text+0x55b): undefined reference to `gzgets'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzflush':
> znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzeof':
> znzlib.c:(.text+0x623): undefined reference to `gzeof'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputc':
> znzlib.c:(.text+0x677): undefined reference to `gzputc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgetc':
> znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzprintf':
> znzlib.c:(.text+0x798): undefined reference to `gzprintf'
> collect2: error: ld returned 1 exit status
> minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for target 'minctools/conversion/nii2mnc' failed
> make[2]: *** [minctools/conversion/nii2mnc] Error 1
> CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all' failed
> make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
> 
> _______________________________________________
> 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 robert.d.vincent at mcgill.ca  Tue Jul 26 23:36:34 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Tue, 26 Jul 2016 23:36:34 -0400
Subject: [MINC-users] dcm2mnc error regarding PatientAge
In-Reply-To: <CALZEBsYNOnpxS-opkovO6mJFu1Xf-a1BeHjHNYbdPxNPLdz0Uw@mail.gmail.com>
References: <CALZEBsYNOnpxS-opkovO6mJFu1Xf-a1BeHjHNYbdPxNPLdz0Uw@mail.gmail.com>
Message-ID: <CAAd5DeQz2bmP8UkREuQeOA3WJDxoyLnhcW59JiycLpoV-YFNSw@mail.gmail.com>

Hi,

I'll relax the test and make it a warning. But the AS VR does not permit a
field value of 0000.

    -bert

On Tue, Jul 26, 2016 at 1:05 PM, Daniel Marchand <daniel at biospective.com>
wrote:

> Hi,
>
> I'm having trouble converting a dicom file including the line:
> (0010,1010) AS [0000]                                   #   4, 1 PatientAge
>
> which throws the error:
> Age units (0000) unknown
>
> It seems that the cause of the error is
> inside of conversion/dcm2mnc/minc_file.c :
>
>     if (strlen(general_info->patient.age) > 0) {
>         string_t temp;
>         int i;
>         double age;
>
>         strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
>         while (temp[i] != 0 && !isdigit(temp[i]))
>           i++;
>         if (temp[i] == 0) {
>           fprintf(stderr, "ERROR: Age was not numeric!!\n");
>           exit(-1);
>         }
>         age = atof(&temp[i]);
>         while (temp[i] != 0 && isdigit(temp[i]))
>           i++;
>         if (temp[i] == 'M')     /* age is in months */
>           age /= 12.0;
>         else if (temp[i] == 'W')   /* age is in weeks */
>           age /= 52.0;
>         else if (temp[i] == 'D')   /* age is in days */
>           age /= 365.0;
>         else if (temp[i] != 'Y') { /* age is in years */
>           fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
>           exit(-1);
>         }
>         miattputdbl(mincid, varid, MIage, age);
>
> I would appear that perhaps a new option could be added where
> dcm2mnc doesn't crash if the age is written as [0000]?
>
> Best,
>
> Daniel
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From thomas.funck at mail.mcgill.ca  Thu Jul 28 22:18:48 2016
From: thomas.funck at mail.mcgill.ca (Thomas Funck, Mr)
Date: Fri, 29 Jul 2016 02:18:48 +0000
Subject: [MINC-users] MINC-users Digest, Vol 131, Issue 14
In-Reply-To: <mailman.3.1469635201.14522.minc-users@bic.mni.mcgill.ca>
References: <mailman.3.1469635201.14522.minc-users@bic.mni.mcgill.ca>
Message-ID: <BN3PR03MB1445B8A770A11A1E52D5AB64A6010@BN3PR03MB1445.namprd03.prod.outlook.com>

Compiling ZLIB before the rest didn't work, but I found a rather hacky workaround.


In the following files the path to libz.a has to be moved to be behind the path to libznz.a.


./minctools/conversion/CMakeFiles/nii2mnc.dir/link.txt
./minctools/conversion/CMakeFiles/mnc2nii.dir/link.txt

After that the compilation works.

Thomas


________________________________
From: minc-users-bounces at bic.mni.mcgill.ca <minc-users-bounces at bic.mni.mcgill.ca> on behalf of minc-users-request at bic.mni.mcgill.ca <minc-users-request at bic.mni.mcgill.ca>
Sent: Wednesday, July 27, 2016 12:00:01 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 131, Issue 14

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. dcm2mnc error regarding PatientAge (Daniel Marchand)
   2. Problem with ZLIB when compiling minc-toolkit-v2
      (Thomas Funck, Mr)
   3. Re: Problem with ZLIB when compiling minc-toolkit-v2
      (vladimir.fonov at gmail.com)
   4. Re: dcm2mnc error regarding PatientAge (Robert D. Vincent)


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

Message: 1
Date: Tue, 26 Jul 2016 13:05:35 -0400
From: Daniel Marchand <daniel at biospective.com>
To: minc-users at bic.mni.mcgill.ca
Subject: [MINC-users] dcm2mnc error regarding PatientAge
Message-ID:
        <CALZEBsYNOnpxS-opkovO6mJFu1Xf-a1BeHjHNYbdPxNPLdz0Uw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

I'm having trouble converting a dicom file including the line:
(0010,1010) AS [0000]                                   #   4, 1 PatientAge

which throws the error:
Age units (0000) unknown

It seems that the cause of the error is
inside of conversion/dcm2mnc/minc_file.c :

    if (strlen(general_info->patient.age) > 0) {
        string_t temp;
        int i;
        double age;

        strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
        while (temp[i] != 0 && !isdigit(temp[i]))
          i++;
        if (temp[i] == 0) {
          fprintf(stderr, "ERROR: Age was not numeric!!\n");
          exit(-1);
        }
        age = atof(&temp[i]);
        while (temp[i] != 0 && isdigit(temp[i]))
          i++;
        if (temp[i] == 'M')     /* age is in months */
          age /= 12.0;
        else if (temp[i] == 'W')   /* age is in weeks */
          age /= 52.0;
        else if (temp[i] == 'D')   /* age is in days */
          age /= 365.0;
        else if (temp[i] != 'Y') { /* age is in years */
          fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
          exit(-1);
        }
        miattputdbl(mincid, varid, MIage, age);

I would appear that perhaps a new option could be added where
dcm2mnc doesn't crash if the age is written as [0000]?

Best,

Daniel


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

Message: 2
Date: Tue, 26 Jul 2016 18:36:14 +0000
From: "Thomas Funck, Mr" <thomas.funck at mail.mcgill.ca>
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] Problem with ZLIB when compiling minc-toolkit-v2
Message-ID:
        <BN3PR03MB1445BC1E1A497B51E9AB82E1A60E0 at BN3PR03MB1445.namprd03.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Hi,

I'm trying to compile minc-toolkit-v2, but ran into the following problem. I'm trying to compile on Ubuntu 16.04.1 LTS and with USE_SYSTEM_ZLIB=OFF. I also tried minc-toolkit but ran into the same error.

Thanks for any help,

Thomas

Scanning dependencies of target nii2mnc
[ 23%] Building C object minctools/conversion/CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
[ 23%] Linking C executable nii2mnc
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzopen':
znzlib.c:(.text+0x4a): undefined reference to `gzopen'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzdopen':
znzlib.c:(.text+0x102): undefined reference to `gzdopen'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `Xznzclose':
znzlib.c:(.text+0x166): undefined reference to `gzclose'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzread':
znzlib.c:(.text+0x220): undefined reference to `gzread'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzwrite':
znzlib.c:(.text+0x320): undefined reference to `gzwrite'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzseek':
znzlib.c:(.text+0x3db): undefined reference to `gzseek'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzrewind':
znzlib.c:(.text+0x447): undefined reference to `gzseek'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znztell':
znzlib.c:(.text+0x4a3): undefined reference to `gztell'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputs':
znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgets':
znzlib.c:(.text+0x55b): undefined reference to `gzgets'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzflush':
znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzeof':
znzlib.c:(.text+0x623): undefined reference to `gzeof'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputc':
znzlib.c:(.text+0x677): undefined reference to `gzputc'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgetc':
znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzprintf':
znzlib.c:(.text+0x798): undefined reference to `gzprintf'
collect2: error: ld returned 1 exit status
minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for target 'minctools/conversion/nii2mnc' failed
make[2]: *** [minctools/conversion/nii2mnc] Error 1
CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all' failed
make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2



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

Message: 3
Date: Tue, 26 Jul 2016 14:43:17 -0400
From: vladimir.fonov at gmail.com
To: MINC list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] Problem with ZLIB when compiling
        minc-toolkit-v2
Message-ID: <64C52D64-4ED0-4241-A956-8952D5B37DF9 at gmail.com>
Content-Type: text/plain; charset=utf-8

Can you try running ?make ZLIB? first , and then ?make nii2mnc? ?


> On Jul 26, 2016, at 14:36, Thomas Funck, Mr <thomas.funck at mail.mcgill.ca> wrote:
>
> Hi,
>
> I'm trying to compile minc-toolkit-v2, but ran into the following problem. I'm trying to compile on Ubuntu 16.04.1 LTS and with USE_SYSTEM_ZLIB=OFF. I also tried minc-toolkit but ran into the same error.
>
> Thanks for any help,
>
> Thomas
>
> Scanning dependencies of target nii2mnc
> [ 23%] Building C object minctools/conversion/CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
> [ 23%] Linking C executable nii2mnc
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzopen':
> znzlib.c:(.text+0x4a): undefined reference to `gzopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzdopen':
> znzlib.c:(.text+0x102): undefined reference to `gzdopen'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `Xznzclose':
> znzlib.c:(.text+0x166): undefined reference to `gzclose'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzread':
> znzlib.c:(.text+0x220): undefined reference to `gzread'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzwrite':
> znzlib.c:(.text+0x320): undefined reference to `gzwrite'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzseek':
> znzlib.c:(.text+0x3db): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzrewind':
> znzlib.c:(.text+0x447): undefined reference to `gzseek'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znztell':
> znzlib.c:(.text+0x4a3): undefined reference to `gztell'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputs':
> znzlib.c:(.text+0x4f7): undefined reference to `gzputs'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgets':
> znzlib.c:(.text+0x55b): undefined reference to `gzgets'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzflush':
> znzlib.c:(.text+0x5c5): undefined reference to `gzflush'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzeof':
> znzlib.c:(.text+0x623): undefined reference to `gzeof'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzputc':
> znzlib.c:(.text+0x677): undefined reference to `gzputc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzgetc':
> znzlib.c:(.text+0x6f5): undefined reference to `gzgetc'
> ../../external//usr/local/minc/lib/libznz.a(znzlib.o): In function `znzprintf':
> znzlib.c:(.text+0x798): undefined reference to `gzprintf'
> collect2: error: ld returned 1 exit status
> minctools/conversion/CMakeFiles/nii2mnc.dir/build.make:105: recipe for target 'minctools/conversion/nii2mnc' failed
> make[2]: *** [minctools/conversion/nii2mnc] Error 1
> CMakeFiles/Makefile2:5017: recipe for target 'minctools/conversion/CMakeFiles/nii2mnc.dir/all' failed
> make[1]: *** [minctools/conversion/CMakeFiles/nii2mnc.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> _______________________________________________
> 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






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

Message: 4
Date: Tue, 26 Jul 2016 23:36:34 -0400
From: "Robert D. Vincent" <robert.d.vincent at mcgill.ca>
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] dcm2mnc error regarding PatientAge
Message-ID:
        <CAAd5DeQz2bmP8UkREuQeOA3WJDxoyLnhcW59JiycLpoV-YFNSw at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

I'll relax the test and make it a warning. But the AS VR does not permit a
field value of 0000.

    -bert

On Tue, Jul 26, 2016 at 1:05 PM, Daniel Marchand <daniel at biospective.com>
wrote:

> Hi,
>
> I'm having trouble converting a dicom file including the line:
> (0010,1010) AS [0000]                                   #   4, 1 PatientAge
>
> which throws the error:
> Age units (0000) unknown
>
> It seems that the cause of the error is
> inside of conversion/dcm2mnc/minc_file.c :
>
>     if (strlen(general_info->patient.age) > 0) {
>         string_t temp;
>         int i;
>         double age;
>
>         strncpy(temp, general_info->patient.age, STRING_T_LEN - 1);
>         while (temp[i] != 0 && !isdigit(temp[i]))
>           i++;
>         if (temp[i] == 0) {
>           fprintf(stderr, "ERROR: Age was not numeric!!\n");
>           exit(-1);
>         }
>         age = atof(&temp[i]);
>         while (temp[i] != 0 && isdigit(temp[i]))
>           i++;
>         if (temp[i] == 'M')     /* age is in months */
>           age /= 12.0;
>         else if (temp[i] == 'W')   /* age is in weeks */
>           age /= 52.0;
>         else if (temp[i] == 'D')   /* age is in days */
>           age /= 365.0;
>         else if (temp[i] != 'Y') { /* age is in years */
>           fprintf(stderr, "ERROR: Age units (%s) unknown.\n", temp);
>           exit(-1);
>         }
>         miattputdbl(mincid, varid, MIage, age);
>
> I would appear that perhaps a new option could be added where
> dcm2mnc doesn't crash if the age is written as [0000]?
>
> Best,
>
> Daniel
> _______________________________________________
> 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 131, Issue 14
*******************************************