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fristed / BEaST

C implementation of Brain Extraction based on nonlocal Segmentation Technique
http://www.bic.mni.mcgill.ca/BEaST
GNU General Public License v3.0
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VIO_OK undeclared error on Ubuntu 12.04 #2

Open jpellman opened 8 years ago

jpellman commented 8 years ago

Hello,

I am attempting to compile BEaST 1.16 on Ubuntu 12.04. However, I am getting the following error when I run make:

[ 76%] Building C object CMakeFiles/beast.dir/mincio.o /tmp/BEaST-release-1.16.00/mincio.c: In function ‘read_minc’: /tmp/BEaST-release-1.16.00/mincio.c:136:120: error: ‘VIO_OK’ undeclared (first use in this function) /tmp/BEaST-release-1.16.00/mincio.c:136:120: note: each undeclared identifier is reported only once for each function it appears in make[2]: * [CMakeFiles/beast.dir/mincio.o] Error 1 make[1]: * [CMakeFiles/beast.dir/all] Error 2 make: *\ [all] Error 2

LIBMINC_DIR is pointing to the directory containing 'LIBMINCConfig.cmake' and NIFTI_ROOT is set to /usr (since I installed the libnifti-dev package). Any idea what the problem might be?

Many thanks, John Pellman

fristed commented 8 years ago

It seems that minc / volume_io header files are not found. Try setting your CFLAGS environment variable to: -I

Simon

On Mon, Feb 1, 2016 at 4:34 PM, John Pellman notifications@github.com wrote:

Hello,

I am attempting to compile BEaST 1.16 on Ubuntu 12.04. However, I am getting the following error when I run make:

[ 76%] Building C object CMakeFiles/beast.dir/mincio.o /tmp/BEaST-release-1.16.00/mincio.c: In function ‘read_minc’: /tmp/BEaST-release-1.16.00/mincio.c:136:120: error: ‘VIO_OK’ undeclared (first use in this function) /tmp/BEaST-release-1.16.00/mincio.c:136:120: note: each undeclared identifier is reported only once for each function it appears in make[2]: * [CMakeFiles/beast.dir/mincio.o] Error 1 make[1]: * [CMakeFiles/beast.dir/all] Error 2 make: *\ [all] Error 2

LIBMINC_DIR is pointing to the directory containing 'LIBMINCConfig.cmake' and NIFTI_ROOT is set to /usr (since I installed the libnifti-dev package). Any idea what the problem might be?

Many thanks, John Pellman

— Reply to this email directly or view it on GitHub https://github.com/fristed/BEaST/issues/2.

jpellman commented 8 years ago

Hi Simon,

I tried setting the CFLAGS variable, but with no luck. I looked in the header files, but couldn't find any variable named VIO_OK defined. The version of MINC we have installed is 0.3.16-20121113 - should this be compatible with BEaST 1.16?

fristed commented 8 years ago

Hi John,

The MINC package is obsolete. You should be using libminc, https://github.com/BIC-MNI/libminc Alternatively, you can install minc toolkit, https://github.com/BIC-MNI/minc-toolkit-v2 - this includes BEaST along with many other tools. There is even an Ubuntu package (though it may not be the latest version of the tools): https://www.mcgill.ca/bic/software/minc/minctoolkit

Simon

On Mon, Feb 1, 2016 at 5:05 PM, John Pellman notifications@github.com wrote:

Hi Simon,

I tried setting the CFLAGS variable, but with no luck. I looked in the header files, but couldn't find any variable named VIO_OK defined. The version of MINC we have installed is 0.3.16-20121113 - should this be compatible with BEaST 1.16?

— Reply to this email directly or view it on GitHub https://github.com/fristed/BEaST/issues/2#issuecomment-178045226.