Re: [Freesurfer] Build problem

2016-12-02 Thread Z K
I was told its be an MNI structure... found in the dependency package 
undercentos6-x86_64-packages/mni, and build from this source tarball:

 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mni.srcbuild.June2015.tgz

On 12/02/2016 05:45 PM, Melvin Robinson wrote:
>
> OK, this sounds good.  Where is General_transform defined?  I could try to 
> find a fix.
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Z K 
> 
> Sent: Friday, December 2, 2016 4:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Build problem
>
> My guess is its a compatibility issue with the dependency package and
> Fedora 23. Although I would have guessed it would have worked, the build
> instructions have only been tested on Ubuntu, Debian and CentOS distros.
>
> I will install Fedora23 on laptop to see if I can properly diagnose the
> issue, but it may take a few days to fit in the schedule.
>
> On 12/02/2016 05:24 PM, Melvin Robinson wrote:
>> OK the OS is Fedora 23 and here is my configure line:
>>
>> ./configure --with-pkgs-dir=../dependencies/centos6-x86_64-packages 
>> --disable-Werror
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Z K 
>> 
>> Sent: Friday, December 2, 2016 4:21 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Build problem
>>
>> What operating system are you using and what is the exact configure command?
>>
>> On 12/02/2016 04:49 PM, Melvin Robinson wrote:
>>> I'm having a small (?) build problem with freesurfer.  My configure line
>>> merely points to the dependencies package and the--disable-Werror flag,
>>> but I get the following error.  Grepping through the source I cannot
>>> find where the structure is defined.
>>>
>>>
>>> gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g
>>> -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI
>>> -fdata-sections -ffunction-sections -Wl,--gc-sections
>>> -I../dependencies/centos6-x86_64-packages/mni/current/include   -MT
>>> oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
>>> In file included from ../include/transform.h:84:0,
>>>  from ../include/mrisurf.h:209,
>>>  from oglutil.c:43:
>>> ../include/mri.h:210:3: error: unknown type name ‘General_transform’
>>>General_transform transform ;   /* the next two are from this struct */
>>>^
>>> ../include/mri.h:211:3: error: unknown type name ‘Transform’
>>>Transform *linear_transform ;
>>>^
>>> ../include/mri.h:212:3: error: unknown type name ‘Transform’
>>>Transform *inverse_linear_transform ;
>>>^
>>> ../include/mri.h:386:35: error: unknown type name ‘General_transform’
>>>  int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
>>>^
>>> In file included from ../include/mrisurf.h:1793:0,
>>>  from oglutil.c:43:
>>> ../include/label.h:54:3: error: unknown type name ‘General_transform’
>>>General_transform transform ;   /* the next two are from this struct */
>>>^
>>> ../include/label.h:55:3: error: unknown type name ‘Transform’
>>>Transform *linear_transform ;
>>>^
>>> ../include/label.h:56:3: error: unknown type name ‘Transform’
>>>Transform *inverse_linear_transform ;
>>>^
>>> In file included from ../include/transform.h:84:0,
>>>  from ../include/mrisurf.h:209,
>>>  from oglutil.c:43:
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIF-g&c=e7TYJBzRfB0YbjEn2u3vBA&r=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus&m=JzCKuEcFeG7YOuPKja3hihjR7T-_j7C1XNNos2d5Lqg&s=pJysyE-V31Vn3dAFzCEOkobl3iTSbt1bafA_u1Dcqbs&e=
>>>
>> ___
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Re: [Freesurfer] Build problem

2016-12-02 Thread Melvin Robinson

OK, this sounds good.  Where is General_transform defined?  I could try to find 
a fix.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Z K 

Sent: Friday, December 2, 2016 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Build problem

My guess is its a compatibility issue with the dependency package and
Fedora 23. Although I would have guessed it would have worked, the build
instructions have only been tested on Ubuntu, Debian and CentOS distros.

I will install Fedora23 on laptop to see if I can properly diagnose the
issue, but it may take a few days to fit in the schedule.

On 12/02/2016 05:24 PM, Melvin Robinson wrote:
> OK the OS is Fedora 23 and here is my configure line:
>
> ./configure --with-pkgs-dir=../dependencies/centos6-x86_64-packages 
> --disable-Werror
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Z K 
> 
> Sent: Friday, December 2, 2016 4:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Build problem
>
> What operating system are you using and what is the exact configure command?
>
> On 12/02/2016 04:49 PM, Melvin Robinson wrote:
>> I'm having a small (?) build problem with freesurfer.  My configure line
>> merely points to the dependencies package and the--disable-Werror flag,
>> but I get the following error.  Grepping through the source I cannot
>> find where the structure is defined.
>>
>>
>> gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g
>> -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI
>> -fdata-sections -ffunction-sections -Wl,--gc-sections
>> -I../dependencies/centos6-x86_64-packages/mni/current/include   -MT
>> oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
>> In file included from ../include/transform.h:84:0,
>>  from ../include/mrisurf.h:209,
>>  from oglutil.c:43:
>> ../include/mri.h:210:3: error: unknown type name ‘General_transform’
>>General_transform transform ;   /* the next two are from this struct */
>>^
>> ../include/mri.h:211:3: error: unknown type name ‘Transform’
>>Transform *linear_transform ;
>>^
>> ../include/mri.h:212:3: error: unknown type name ‘Transform’
>>Transform *inverse_linear_transform ;
>>^
>> ../include/mri.h:386:35: error: unknown type name ‘General_transform’
>>  int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
>>^
>> In file included from ../include/mrisurf.h:1793:0,
>>  from oglutil.c:43:
>> ../include/label.h:54:3: error: unknown type name ‘General_transform’
>>General_transform transform ;   /* the next two are from this struct */
>>^
>> ../include/label.h:55:3: error: unknown type name ‘Transform’
>>Transform *linear_transform ;
>>^
>> ../include/label.h:56:3: error: unknown type name ‘Transform’
>>Transform *inverse_linear_transform ;
>>^
>> In file included from ../include/transform.h:84:0,
>>  from ../include/mrisurf.h:209,
>>  from oglutil.c:43:
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIF-g&c=e7TYJBzRfB0YbjEn2u3vBA&r=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus&m=JzCKuEcFeG7YOuPKja3hihjR7T-_j7C1XNNos2d5Lqg&s=pJysyE-V31Vn3dAFzCEOkobl3iTSbt1bafA_u1Dcqbs&e=
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIF-g&c=e7TYJBzRfB0YbjEn2u3vBA&r=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus&m=JzCKuEcFeG7YOuPKja3hihjR7T-_j7C1XNNos2d5Lqg&s=pJysyE-V31Vn3dAFzCEOkobl3iTSbt1bafA_u1Dcqbs&e=
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
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>   . If the

Re: [Freesurfer] Build problem

2016-12-02 Thread Z K
My guess is its a compatibility issue with the dependency package and 
Fedora 23. Although I would have guessed it would have worked, the build 
instructions have only been tested on Ubuntu, Debian and CentOS distros.

I will install Fedora23 on laptop to see if I can properly diagnose the 
issue, but it may take a few days to fit in the schedule.

On 12/02/2016 05:24 PM, Melvin Robinson wrote:
> OK the OS is Fedora 23 and here is my configure line:
>
> ./configure --with-pkgs-dir=../dependencies/centos6-x86_64-packages 
> --disable-Werror
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Z K 
> 
> Sent: Friday, December 2, 2016 4:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Build problem
>
> What operating system are you using and what is the exact configure command?
>
> On 12/02/2016 04:49 PM, Melvin Robinson wrote:
>> I'm having a small (?) build problem with freesurfer.  My configure line
>> merely points to the dependencies package and the--disable-Werror flag,
>> but I get the following error.  Grepping through the source I cannot
>> find where the structure is defined.
>>
>>
>> gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g
>> -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI
>> -fdata-sections -ffunction-sections -Wl,--gc-sections
>> -I../dependencies/centos6-x86_64-packages/mni/current/include   -MT
>> oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
>> In file included from ../include/transform.h:84:0,
>>  from ../include/mrisurf.h:209,
>>  from oglutil.c:43:
>> ../include/mri.h:210:3: error: unknown type name ‘General_transform’
>>General_transform transform ;   /* the next two are from this struct */
>>^
>> ../include/mri.h:211:3: error: unknown type name ‘Transform’
>>Transform *linear_transform ;
>>^
>> ../include/mri.h:212:3: error: unknown type name ‘Transform’
>>Transform *inverse_linear_transform ;
>>^
>> ../include/mri.h:386:35: error: unknown type name ‘General_transform’
>>  int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
>>^
>> In file included from ../include/mrisurf.h:1793:0,
>>  from oglutil.c:43:
>> ../include/label.h:54:3: error: unknown type name ‘General_transform’
>>General_transform transform ;   /* the next two are from this struct */
>>^
>> ../include/label.h:55:3: error: unknown type name ‘Transform’
>>Transform *linear_transform ;
>>^
>> ../include/label.h:56:3: error: unknown type name ‘Transform’
>>Transform *inverse_linear_transform ;
>>^
>> In file included from ../include/transform.h:84:0,
>>  from ../include/mrisurf.h:209,
>>  from oglutil.c:43:
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIF-g&c=e7TYJBzRfB0YbjEn2u3vBA&r=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus&m=JzCKuEcFeG7YOuPKja3hihjR7T-_j7C1XNNos2d5Lqg&s=pJysyE-V31Vn3dAFzCEOkobl3iTSbt1bafA_u1Dcqbs&e=
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIF-g&c=e7TYJBzRfB0YbjEn2u3vBA&r=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus&m=JzCKuEcFeG7YOuPKja3hihjR7T-_j7C1XNNos2d5Lqg&s=pJysyE-V31Vn3dAFzCEOkobl3iTSbt1bafA_u1Dcqbs&e=
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] Build problem

2016-12-02 Thread Melvin Robinson
OK the OS is Fedora 23 and here is my configure line:

./configure --with-pkgs-dir=../dependencies/centos6-x86_64-packages 
--disable-Werror



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Z K 

Sent: Friday, December 2, 2016 4:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Build problem

What operating system are you using and what is the exact configure command?

On 12/02/2016 04:49 PM, Melvin Robinson wrote:
> I'm having a small (?) build problem with freesurfer.  My configure line
> merely points to the dependencies package and the--disable-Werror flag,
> but I get the following error.  Grepping through the source I cannot
> find where the structure is defined.
>
>
> gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g
> -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI
> -fdata-sections -ffunction-sections -Wl,--gc-sections
> -I../dependencies/centos6-x86_64-packages/mni/current/include   -MT
> oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
> In file included from ../include/transform.h:84:0,
>  from ../include/mrisurf.h:209,
>  from oglutil.c:43:
> ../include/mri.h:210:3: error: unknown type name ‘General_transform’
>General_transform transform ;   /* the next two are from this struct */
>^
> ../include/mri.h:211:3: error: unknown type name ‘Transform’
>Transform *linear_transform ;
>^
> ../include/mri.h:212:3: error: unknown type name ‘Transform’
>Transform *inverse_linear_transform ;
>^
> ../include/mri.h:386:35: error: unknown type name ‘General_transform’
>  int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
>^
> In file included from ../include/mrisurf.h:1793:0,
>  from oglutil.c:43:
> ../include/label.h:54:3: error: unknown type name ‘General_transform’
>General_transform transform ;   /* the next two are from this struct */
>^
> ../include/label.h:55:3: error: unknown type name ‘Transform’
>Transform *linear_transform ;
>^
> ../include/label.h:56:3: error: unknown type name ‘Transform’
>Transform *inverse_linear_transform ;
>^
> In file included from ../include/transform.h:84:0,
>  from ../include/mrisurf.h:209,
>  from oglutil.c:43:
>
>
> ___
> Freesurfer mailing list
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>
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Re: [Freesurfer] Build problem

2016-12-02 Thread Z K
What operating system are you using and what is the exact configure command?

On 12/02/2016 04:49 PM, Melvin Robinson wrote:
> I'm having a small (?) build problem with freesurfer.  My configure line
> merely points to the dependencies package and the--disable-Werror flag,
> but I get the following error.  Grepping through the source I cannot
> find where the structure is defined.
>
>
> gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g
> -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI
> -fdata-sections -ffunction-sections -Wl,--gc-sections
> -I../dependencies/centos6-x86_64-packages/mni/current/include   -MT
> oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
> In file included from ../include/transform.h:84:0,
>  from ../include/mrisurf.h:209,
>  from oglutil.c:43:
> ../include/mri.h:210:3: error: unknown type name ‘General_transform’
>General_transform transform ;   /* the next two are from this struct */
>^
> ../include/mri.h:211:3: error: unknown type name ‘Transform’
>Transform *linear_transform ;
>^
> ../include/mri.h:212:3: error: unknown type name ‘Transform’
>Transform *inverse_linear_transform ;
>^
> ../include/mri.h:386:35: error: unknown type name ‘General_transform’
>  int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
>^
> In file included from ../include/mrisurf.h:1793:0,
>  from oglutil.c:43:
> ../include/label.h:54:3: error: unknown type name ‘General_transform’
>General_transform transform ;   /* the next two are from this struct */
>^
> ../include/label.h:55:3: error: unknown type name ‘Transform’
>Transform *linear_transform ;
>^
> ../include/label.h:56:3: error: unknown type name ‘Transform’
>Transform *inverse_linear_transform ;
>^
> In file included from ../include/transform.h:84:0,
>  from ../include/mrisurf.h:209,
>  from oglutil.c:43:
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



[Freesurfer] Build problem

2016-12-02 Thread Melvin Robinson
I'm having a small (?) build problem with freesurfer.  My configure line merely 
points to the dependencies package and the--disable-Werror flag, but I get the 
following error.  Grepping through the source I cannot find where the structure 
is defined.


gcc -DHAVE_CONFIG_H -I. -I..  -I../include -pthread  -DHAVE_OPENGL -g -O3 
-msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI 
-fdata-sections -ffunction-sections -Wl,--gc-sections 
-I../dependencies/centos6-x86_64-packages/mni/current/include   -MT oglutil.o 
-MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c
In file included from ../include/transform.h:84:0,
 from ../include/mrisurf.h:209,
 from oglutil.c:43:
../include/mri.h:210:3: error: unknown type name 'General_transform'
   General_transform transform ;   /* the next two are from this struct */
   ^
../include/mri.h:211:3: error: unknown type name 'Transform'
   Transform *linear_transform ;
   ^
../include/mri.h:212:3: error: unknown type name 'Transform'
   Transform *inverse_linear_transform ;
   ^
../include/mri.h:386:35: error: unknown type name 'General_transform'
 int   MRIsetTransform(MRI *mri,   General_transform *transform) ;
   ^
In file included from ../include/mrisurf.h:1793:0,
 from oglutil.c:43:
../include/label.h:54:3: error: unknown type name 'General_transform'
   General_transform transform ;   /* the next two are from this struct */
   ^
../include/label.h:55:3: error: unknown type name 'Transform'
   Transform *linear_transform ;
   ^
../include/label.h:56:3: error: unknown type name 'Transform'
   Transform *inverse_linear_transform ;
   ^
In file included from ../include/transform.h:84:0,
 from ../include/mrisurf.h:209,
 from oglutil.c:43:
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