from:"Melvin Robinson"

[Freesurfer] KWWidgets

2018-02-26 Thread Melvin Robinson

A FreeSurfer build from source requires KWWidgets, but it has been deprecated 
for 10 years.  What does Freesurfer use this code for?
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Re: [Freesurfer] Cuda version > 5.0

2018-02-08 Thread Melvin Robinson

Yes, Freesurfer 6 works well with CUDA 9.1.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Melanie Ganz 

Sent: Thursday, February 8, 2018 10:54 AM
To: Freesurfer support list
Subject: [Freesurfer] Cuda version > 5.0

Dear FS list,

we just got a really nice graphics card (Quadro P6000) that we also
would like to use to speed up recon-all, preferably for running high-res
data with FS version 6. Now we know that in the precompiled FS version 6
it still looks for cuda 5.0, but it seems like some people have gotten
it to work with 8.0 (see e.g. here
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2017-2DMay_052047.html=DwIBAg=e7TYJBzRfB0YbjEn2u3vBA=OUdSsFeBuoDPVT3xBQdPDIuLL-safdr4PHYIlKkdkus=h70l-aJ2xIrLjRDQvds1wqaaNCl_-Fk7hd1I4Wkib9w=a-j4gSWmwY7hyzTLkGtyX0dK4e0hTeKoLpxWaTaNKVA=).

Has anyone gotten FS version 6 compiled with cuda 9.1?

Cheers,

Melanie

--
Melanie Ganz-Benjaminsen, MSc, Ph.D.
Neurobiology Research Unit
University of Copenhagen
Rigshospitalet
Rockefeller Center
Juliane Maries Vej 28/30, 3.
DK-2100 Copenhagen
Denmark

phone:  +45 3545 6718
e-mail: melanie.g...@nru.dk
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Re: [Freesurfer] How to compile FreeSurfer with CUDA?

2018-02-05 Thread Melvin Robinson

Once upon a time I had many problems with OpenGL/GLU problems in my FreeSurfer 
build.  Ultimately the problem was that the version of GLU installed with Mesa 
package was not really compatible with the compiler that I was using.   After 
straightening this problem out using the configure option --with-cuda allowed 
me to build with CUDA 9.1 with no problems.


What is your setup?  Compilers?  GPU?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of markus.mert...@evkb.de 

Sent: Monday, February 5, 2018 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to compile FreeSurfer with CUDA?

Hello Freesurfer experts,

I am trying to compile FreeSurfer to make use of its CUDA capabilities. The 
precompiled version does not run on my system. But when I try to compile 
FreeSurfer I get the following error:

# ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages 
--enable-fermi-gpu
...
configure: Getting OpenGL info...
checking GL directory... gl directory is /usr/include
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenGL library... no
configure: error: FATAL: GL not found, but needed for  tcltkapps XawPlusapps 
kwwapps wxwapps. Use --with-gl-dir=... to specify


But OpenGL is installed:

# ll /usr/lib64/libGL.so*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so -> 
libGL.so.1.2.0*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so.1 -> 
libGL.so.1.2.0*
-rwxr-xr-x 1 root root 452752 Jan 15 23:37 /usr/lib64/libGL.so.1.2.0*
# ll /usr/include/GL/gl.h
-rw-r--r-- 1 root root 80615 Jan 15 23:35 /usr/include/GL/gl.h
#


The configure script did not ask for CUDA, yet. But CUDA is also installed in 
/usr/lib64:

# ll /usr/lib64/libcuda*
-rw-r--r-- 1 root root 556000 Jan 13  2017 /usr/lib64/libcudadevrt.a
lrwxrwxrwx 1 root root 16 Jan 13  2017 /usr/lib64/libcudart.so -> 
libcudart.so.8.0*
lrwxrwxrwx 1 root root 19 Jan 13  2017 /usr/lib64/libcudart.so.8.0 -> 
libcudart.so.8.0.61*
-rwxr-xr-x 1 root root 415432 Jan 13  2017 /usr/lib64/libcudart.so.8.0.61*
-rw-r--r-- 1 root root 775162 Jan 13  2017 /usr/lib64/libcudart_static.a
#


Adding the option  "--with-gl-dir=/usr/lib64" to the configure script does not 
help. What else could I try?

Regards,

Markus


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[Freesurfer] OpenGL link errors

2017-12-22 Thread Melvin Robinson

I posted this to the Freesurfer github site, but didn't exactly know if that 
was the most appropriate place.


The Freesurfer build fails at this command:
libtool: link: g++ -fdata-sections -ffunction-sections -Wl,--gc-sections 
-Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mris_show mris_show.o 
/usr/lib64/libuuid.so 
-L/home/melrobin/packages/centos6-x86_64-packages/qt/current/lib -L/usr/lib64
-L/usr/X11R6/lib64 
-L/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib 
-L/home/melrobin/packages/centos6-x86_64-packages//vxl/current/lib 
-L/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit
 ../utils/libutils.a ../minc_substitute/libminc_substitute.a 
../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a 
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a 
../tiff/libtiff.a ../expat/libexpat.a ../glut/libglut.a -L/lib64 -lX11 -lXmu 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKAlgorithms.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKCommon.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNumerics.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKMetaIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKniftiio.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNrrdIO.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkpng.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitksys.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitktiff.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkv3p_netlib.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkzlib.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkgdcm.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkopenjpeg.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg8.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg12.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg16.a
 
/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKDICOMParser.a
 -lz -lm -lcrypt -ldl -lpthread 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libvolume_io.a 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libminc.a 
/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libnetcdf.a 
-lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib

and produces lots of these types of errors
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:878: undefined 
reference to glViewport' mris_show.o: In functionspecial_key_handler':
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:923: undefined 
reference to glMatrixMode' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:937: undefined 
reference toglRotatef'
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:955: undefined 
reference to glRotatef' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:945: undefined 
reference toglRotatef'
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:951: undefined 
reference to glRotatef' 
/home/melrobin/packages/freesurfer/mris_show/mris_show.c:933: undefined 
reference toglRotatef'



The build seems not to include the OpenGL libraries when building mris_show as 
you can see from the link line. I'm trying to trace this up the Autotools 
chain, but need some help. I can work a little more on a fix with a little 
guidance telling me where to look.

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Re: [Freesurfer] STRING type

2016-12-09 Thread Melvin Robinson

There does not appear to be a typedef for it in the MNI dependencies. This 
might be why I'm getting the error.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Friday, December 9, 2016 9:02:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] STRING type

Hi Melvin

it is an MNI datatype I believe
cheers
Bruce
On Fri, 9 Dec 2016, Melvin Robinson wrote:

>
> I'm trying to build Freesurfer from developer sources and am running into
> this error:
>
> mriio.c:3692:27: error: ‘STRING’ undeclared (first use in this function)
>status = output_volume((STRING)fname, nc_data_type, signed_flag, min,
> max,
>
>
> Can you tell me where STRING comes from?  I could not find this datatype
> in either the sources or the dependencies.
>
>
>
>
>

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[Freesurfer] STRING type

2016-12-08 Thread Melvin Robinson

I'm trying to build Freesurfer from developer sources and am running into this 
error:

mriio.c:3692:27: error: 'STRING' undeclared (first use in this function)
   status = output_volume((STRING)fname, nc_data_type, signed_flag, min, max,


Can you tell me where STRING comes from?  I could not find this datatype in 
either the sources or the dependencies.


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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 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K 
<zkauf...@nmr.mgh.harvard.edu>
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 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K 
> <zkauf...@nmr.mgh.harvard.edu>
> 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:
>>
>>
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>>
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>
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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 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K 
<zkauf...@nmr.mgh.harvard.edu>
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:
>
>
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[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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[Freesurfer] CVS repository

2016-11-10 Thread Melvin Robinson

I am trying to checkout the development version of Freesurfer from the CVS 
repository.  I need to build against VTK 7.1 instead of 5.6 for freeview and am 
using these instructions:  https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS

Using this command:

 cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P 
dev


Results in the following error:


cvs server: cannot find module `dev' - ignored

Can you tell me the correct module name?


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[Freesurfer] KWWidgets

Re: [Freesurfer] Cuda version > 5.0

Re: [Freesurfer] How to compile FreeSurfer with CUDA?

[Freesurfer] OpenGL link errors

Re: [Freesurfer] STRING type

[Freesurfer] STRING type

Re: [Freesurfer] Build problem

Re: [Freesurfer] Build problem

[Freesurfer] Build problem

[Freesurfer] CVS repository

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