mnc2nii appears to give incorrect scaling about minc-tools

[matthew-brett]

For reference, the current github source code of nibabel will load MINC files and gives the same values for mean, max, min etc as mincstats on - for example - a small MINC2 file in the repo: https://github.com/nipy/nibabel/blob/master/nibabel/tests/data/small.mnc

[vfonov]

I'll take a look....

Is it the problem in master or develop branch ?

[matthew-brett]

I'm sorry - I was running from an Ubuntu 12.04 install - it may well be that the problem is gone in one of these branches. I haven't succeeded yet in building minc-tools I'm afraid. On Wheezy, my last error was (latest git checkout of libminc and minc-tools:

cd libminc
./autogen.sh
./configure --prefix=/home/mb312/usr/local
make && make install
cd ../minc-tools
 ./autogen.sh 
./configure --prefix=/home/mb312/usr/local --with-minc2
make && make install

leading to:

gcc -DHAVE_CONFIG_H -I. -I./progs/Proglib -I./conversion/Acr_nema    -g -O2 -MT progs/coordinates/voxeltoworld.o -MD -MP -MF $depbase.Tpo -c -o progs/coordinates/voxeltoworld.o progs/coordinates/voxeltoworld.c &&\
mv -f $depbase.Tpo $depbase.Po
progs/coordinates/voxeltoworld.c: In function ‘main’:
progs/coordinates/voxeltoworld.c:137:74: error: ‘VIO_OK’ undeclared (first use in this function)
progs/coordinates/voxeltoworld.c:137:74: note: each undeclared identifier is reported only once for each function it appears in

[vfonov]

Use develop branch , and use cmake for configuring

[matthew-brett]

 cd libminc
 git clean -fxd
 mkdir build
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=/home/mb312/usr/local ..
 make && make install
 cd ../../minc-tools
 git clean -fxd
 mkdir build
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=/home/mb312/usr/local -DLIBMINC_DIR=/home/mb312/dev_trees/libminc/build ..
 make

Causing:

[ 28%] Building C object progs/CMakeFiles/mincmorph.dir/mincmorph/mincmorph.c.o
/home/mb312/dev_trees/minc-tools/progs/mincmorph/mincmorph.c: In function ‘main’:
/home/mb312/dev_trees/minc-tools/progs/mincmorph/mincmorph.c:525:55: error: ‘VIO_OK’ undeclared (first use in this function)
/home/mb312/dev_trees/minc-tools/progs/mincmorph/mincmorph.c:525:55: note: each undeclared identifier is reported only once for each function it appears in
make[2]: *** [progs/CMakeFiles/mincmorph.dir/mincmorph/mincmorph.c.o] Error 1
make[1]: *** [progs/CMakeFiles/mincmorph.dir/all] Error 2
make: *** [all] Error 2

[matthew-brett]

I'll be offline for the next few weeks while I'm in Cuba.

[vfonov]

the error about VIO_OK indicates that mic-tools is from master branch and libminc is from develop branch

[matthew-brett]

Do you mean the other way round? Yes, I was using libminc 'master'

 cd libminc
 git co develop
 git clean -fxd
 git submodule update --init
 mkdir build
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=/home/mb312/usr/local ..
 make && make install
 cd ../../minc-tools
 git co develop
 git clean -fxd
 git submodule update --init
 mkdir build
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=/home/mb312/usr/local -DLIBMINC_DIR=/home/mb312/dev_trees/libminc/build ..
 make

gives:

[  2%] Building C object progs/CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o
Linking C executable minc_modify_header
CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o: In function `main':
minc_modify_header.c:(.text+0x1f2): undefined reference to `miexpand_file'

[vfonov]

You have to enable support for MINC1 : -DLIBMINC_MINC1_SUPPORT:BOOL=ON

[matthew-brett]

[ 95%] Building C object conversion/CMakeFiles/nii2mnc.dir/nifti1/nii2mnc.c.o
/home/mb312/dev_trees/minc-tools/conversion/nifti1/nii2mnc.c: In function ‘main’:
/home/mb312/dev_trees/minc-tools/conversion/nifti1/nii2mnc.c:123:5: error: unknown type name ‘Transform’
/home/mb312/dev_trees/minc-tools/conversion/nifti1/nii2mnc.c:124:5: error: unknown type name ‘General_transform’
/home/mb312/dev_trees/minc-tools/conversion/nifti1/nii2mnc.c:333:7: warning: passing argument 1 of ‘make_identity_transform’ from incompatible pointer type [enabled by default]

[vfonov]

pull the updates , it should compile now

[matthew-brett]

I can't see any recent updates in minc-tools or libminc . Should I be looking somewhere else?

[vfonov]

I merged changes from master into develop, they are older then the last commit to develop , so they don't show up.
In particular this commit is important: 13ebefa

[andrewjanke]

Thanks Vlad,

I'm all for pushing all the current changes from develop to master now
ready for the next release. All the testing I have done on the develop
branch so far has been OK.

a

On 8 September 2013 15:15, Vladimir S. FONOV [email protected]:

I merged changes from master into develop, they are older then the last
commit to develop , so they don't show up.
In particular this commit is important: 13ebefahttps://github.com/BIC-MNI/minc-tools/commit/13ebefae02c6151d9aca0f5d92fb905cf64c20b7

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-24015279
.

[vfonov]

Hmm, somehow there was something going on with VIO_ prefix in nii2mnc - looks like I missed it in last pull request

[gdevenyi]

Tested with latest versions, fixed.