[Mrtrix-discussion] support for MIF & NIfTI GZ compression
Markus Gschwind
markus.gschwind at gmail.com
Sun Mar 18 07:41:35 PDT 2012
Dear Donald!
I found the solution! I just show here how:
>> system('otool -L /usr/local/bin/mrview')
/usr/local/bin/mrview:
lib/libmrtrix-0_2_10.dylib (compatibility version 0.0.0, current version
0.0.0)
/usr/local/lib/libgsl.0.dylib (compatibility version 17.0.0, current
version 17.0.0)
/usr/local/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/local/lib/libgtkmm-2.4.1.dylib (compatibility version 3.0.0, current
version 3.0.0)
/usr/local/lib/libatkmm-1.6.1.dylib (compatibility version 3.0.0, current
version 3.0.0)
/usr/local/lib/libgdkmm-2.4.1.dylib (compatibility version 3.0.0, current
version 3.0.0)
/usr/local/lib/libgiomm-2.4.1.dylib (compatibility version 4.0.0, current
version 4.0.0)
/usr/local/lib/libpangomm-1.4.1.dylib (compatibility version 2.0.0,
current version 2.30.0)
/usr/local/lib/libglibmm-2.4.1.dylib (compatibility version 4.0.0, current
version 4.0.0)
/usr/local/lib/libcairomm-1.0.1.dylib (compatibility version 6.0.0,
current version 6.0.0)
/usr/local/lib/libsigc-2.0.0.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/local/lib/libgtkglext-x11-1.0.0.0.0.dylib (compatibility version
1.0.0, current version 1.0.0)
/usr/local/lib/libgdkglext-x11-1.0.0.0.0.dylib (compatibility version
1.0.0, current version 1.0.0)
/usr/X11/lib/libGLU.1.dylib (compatibility version 1.3.0, current version
1.3.0)
/usr/X11/lib/libGL.1.dylib (compatibility version 1.2.0, current version
1.2.0)
/usr/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version
9.0.0)
/usr/X11/lib/libXt.6.dylib (compatibility version 7.0.0, current version
7.0.0)
/usr/X11/lib/libSM.6.dylib (compatibility version 7.0.0, current version
7.0.0)
/usr/X11/lib/libICE.6.dylib (compatibility version 10.0.0, current version
10.0.0)
/usr/local/lib/libgtk-x11-2.0.0.dylib (compatibility version 2401.0.0,
current version 2401.6.0)
/usr/local/lib/libpangox-1.0.0.dylib (compatibility version 2801.0.0,
current version 2801.4.0)
/usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current version
9.0.0)
/usr/local/lib/libgdk-x11-2.0.0.dylib (compatibility version 2401.0.0,
current version 2401.6.0)
/usr/local/lib/libatk-1.0.0.dylib (compatibility version 20210.0.0,
current version 20210.1.0)
/usr/local/lib/libgio-2.0.0.dylib (compatibility version 2801.0.0, current
version 2801.8.0)
/usr/local/lib/libpangoft2-1.0.0.dylib (compatibility version 2801.0.0,
current version 2801.4.0)
/usr/local/lib/libpangocairo-1.0.0.dylib (compatibility version 2801.0.0,
current version 2801.4.0)
/usr/local/lib/libgdk_pixbuf-2.0.0.dylib (compatibility version 2401.0.0,
current version 2401.0.0)
/usr/X11/lib/libcairo.2.dylib (compatibility version 10803.0.0, current
version 10803.6.0)
/usr/local/lib/libpango-1.0.0.dylib (compatibility version 2801.0.0,
current version 2801.4.0)
/usr/X11/lib/libfreetype.6.dylib (compatibility version 14.0.0, current
version 14.2.0)
/usr/X11/lib/libfontconfig.1.dylib (compatibility version 6.0.0, current
version 6.3.0)
/usr/local/lib/libgobject-2.0.0.dylib (compatibility version 2801.0.0,
current version 2801.8.0)
/usr/local/lib/libgmodule-2.0.0.dylib (compatibility version 2801.0.0,
current version 2801.8.0)
/usr/local/lib/libgthread-2.0.0.dylib (compatibility version 2801.0.0,
current version 2801.8.0)
/usr/local/lib/libglib-2.0.0.dylib (compatibility version 2801.0.0,
current version 2801.8.0)
/usr/local/Cellar/gettext/0.18.1.1/lib/libintl.8.dylib (compatibility
version 10.0.0, current version 10.1.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
7.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
125.2.11)
ans =
0
I also thought that it was MATLAB that loads a wrong libfreetype. I looked
for libfreetype:
>> system('locate libfreetype.6.dylib')
/Applications/Gimp.app/Contents/Resources/lib/libfreetype.6.dylib
/Applications/MATLAB_R2009b.app/bin/maci/libfreetype.6.dylib
/Applications/MATLAB_R2009b.app/bin/maci64/libfreetype.6.dylib
/Applications/Scribus.app/Contents/Frameworks/libfreetype.6.dylib
/Applications/TeX/TeXworks.app/Contents/MacOS/libfreetype.6.dylib
/Applications/VLC.app/Contents/MacOS/lib/libfreetype.6.dylib
/Developer/SDKs/MacOSX10.6.sdk/usr/X11/lib/libfreetype.6.dylib
/usr/X11/lib/libfreetype.6.dylib
ans =
0
and indeed it seems that MATLAB uses a old version:
>> system('otool -L
/Applications/MATLAB_R2009b.app/bin/maci64/libfreetype.6.dylib')
/Applications/MATLAB_R2009b.app/bin/maci64/libfreetype.6.dylib:
@loader_path/libfreetype.dylib (compatibility version 10.0.0, current
version 10.16.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
111.0.0)
ans =
0
I learned that the path for dylib in MATLAB is defined by DYLD_LIBRARY_PATH
>> getenv DYLD_LIBRARY_PATH
ans =
/Applications/MATLAB_R2009b.app/sys/os/maci64:/Applications/MATLAB_R2009b.app/bin/maci64/MATLAB.app/Contents/MacOS:/Applications/MATLAB_R2009b.app/bin/maci64:/Applications/MATLAB_R2009b.app/extern/lib/maci64:/Applications/MATLAB_R2009b.app/runtime/maci64
and I then set the right path:
setenv('DYLD_LIBRARY_PATH', '/usr/X11')
and it worked!!!
>> system('mrview')
Thanks for your help, Donald!!
Best, Markus
2012/3/18 Donald Tournier <d.tournier at brain.org.au>
> Hi Markus,
>
> This latest error you're getting is pretty strange. It looks like mrview
> requires libfreetype version >= 14.0.0, which is exactly what is installed
> (as you checked with otool), but for some strange reason it gets version
> 10.0.0 when launched within matlab.
>
> I have no idea how that can happen, and I'm not familiar enough with
> MacOSX have any sensible suggestions. The only thing I can think of is that
> there may be different versions of the library installed (maybe the older
> one is part of the matlab install?), and somehow the wrong one gets loaded.
> What does system('otool -L mrview') report?
>
> Cheers,
>
> Donald.
>
>
> On 9 March 2012 23:47, Markus Gschwind <markus.gschwind at gmail.com> wrote:
>
>> Dear Donald,
>>
>> I am sorry to get back to that problem once more.
>>
>> Before this update, I could call mrview like any other mrtrix tool from
>> within MATLAB via te 'system' command.
>>
>> Now there is an error of dylib
>>
>> >> system('mrview')
>> dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib
>> Referenced from: /usr/local/bin/mrview
>> Reason: Incompatible library version: mrview requires version 14.0.0 or
>> later, but libfreetype.6.dylib provides version 10.0.0
>> mrview: Trace/breakpoint trap
>>
>> ans =
>>
>> 133
>>
>>
>> However the dylib is actually there:
>>
>>
>> >> system('otool -L /usr/X11/lib/libfreetype.6.dylib')
>> /usr/X11/lib/libfreetype.6.dylib:
>> /usr/X11/lib/libfreetype.6.dylib (compatibility version 14.0.0, current
>> version 14.2.0)
>> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
>> /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version
>> 1.0.5)
>> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
>> (compatibility version 1.0.0, current version 44.0.0)
>> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
>> (compatibility version 1.0.0, current version 38.0.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 125.2.11)
>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
>> (compatibility version 150.0.0, current version 550.44.0)
>>
>> ans =
>>
>> 0
>>
>>
>> It seems that mrview references to an old dylib version? How could I fix
>> that?
>>
>> Thank you so much!
>>
>> Markus
>>
>>
>> 2012/3/9 Markus Gschwind <markus.gschwind at gmail.com>
>>
>>> Dear Donald!
>>>
>>> Sorry for the delayed answer.
>>>
>>> Thank you very much! I did now as you proposed
>>>
>>> "./build clean && ./build && sudo ./build install".
>>>
>>> and indeed this fixed the problem!
>>>
>>> Thank you again for your help, very much appreciated!!
>>> Best, Markus
>>>
>>>
>>>
>>> 2012/3/9 Donald Tournier <d.tournier at brain.org.au>
>>>
>>>> Hi Markus,
>>>>
>>>> I was just looking through your previous email, and there was something
>>>> in the command-line log that looks like it might explain your problem:
>>>>
>>>> Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ tar xvfj
>>>>> mrtrix-patch-GZ.tar.bz2
>>>>> x build
>>>>> x lib/image/format/list.cpp
>>>>> x lib/image/format/mrtrix.cpp
>>>>> x lib/image/format/nifti1.cpp
>>>>> x lib/image/mapper.cpp
>>>>> x lib/image/mapper.h
>>>>> x lib/image/object.cpp
>>>>> x lib/image/object.h
>>>>> x sysconf/linux.py
>>>>> x sysconf/darwin.py
>>>>> x sysconf/windows.py
>>>>> *Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ ./build*
>>>>> *Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ sudo ./build
>>>>> install*
>>>>> installing executables to "/usr/local/mrtrix/bin" and dynamic library
>>>>> to "/usr/local/mrtrix/lib"... ok
>>>>> creating symbolic links to executables in "/usr/local/bin" and to
>>>>> dynamic library in "/usr/local/lib"... ok
>>>>> configuration file already exists - leaving as-is
>>>>> Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$
>>>>>
>>>>
>>>> Looks like the ./build command did nothing, when if should at the very
>>>> least redo the library link stage. So the ./build install would simply copy
>>>> over the existing library, assuming it was built as part of a previous
>>>> unpatched install, and that library would therefore not have support for
>>>> GZ. Easy to fix that, if you simply do "./build clean && ./build && sudo
>>>> ./build install".
>>>>
>>>> Hope that fixes the problem...
>>>> Cheers,
>>>>
>>>> Donald.
>>>>
>>>>
>>>>>
>>>>>
>>>>>
>>>>> However, there seems still to be a problem:
>>>>>
>>>>> Markus-Gschwinds-MacBook-Pro:CONT markus$ mrinfo
>>>>> CONT_dti_FA_space_bin.nii.gz
>>>>> mrinfo: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"
>>>>> mrinfo: error opening image "CONT_dti_FA_space_bin.nii.gz"
>>>>>
>>>>>
>>>>>
>>>>> Markus-Gschwinds-MacBook-Pro:CONT markus$ mrview
>>>>> CONT_dti_FA_space_bin.nii.gz
>>>>>
>>>>> (process:377): Gtk-WARNING **: Locale not supported by C library.
>>>>> Using the fallback 'C' locale.
>>>>> Xlib: extension "RANDR" missing on display
>>>>> "/tmp/launch-29bcMY/org.x:0".
>>>>> mrview: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"
>>>>> mrview: error opening image "CONT_dti_FA_space_bin.nii.gz"
>>>>>
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Markus
>>>>>
>>>>>
>>>>> 2012/3/6 Donald Tournier <d.tournier at brain.org.au>
>>>>>
>>>>>> Hi Markus,
>>>>>>
>>>>>> Ian is spot on, the -lz flags is missing in the library link command,
>>>>>> which for some reason isn't a problem on Linux. It's a simple fix: in the
>>>>>> build script, change line 315 to read:
>>>>>>
>>>>>> '$obj$': [ item for item in self.deps ] + pkg (pkgconfig_glib,
>>>>>> 'libs') + ld_flags_gsl + ld_flags_zlib,
>>>>>>
>>>>>> (i.e. add " + ld_flags_zlib"). I'm attaching a new version of the
>>>>>> patch with the fix included for those who were about to try it out...
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Donald.
>>>>>>
>>>>>>
>>>>>> On 6 March 2012 21:59, Ian Malone <i.malone at ucl.ac.uk> wrote:
>>>>>>
>>>>>>> **
>>>>>>> It looks like zlib isn't getting linked, though the patch does have
>>>>>>> the flag for it, maybe try './build clean' first? Don't have a Mac to test
>>>>>>> on I'm afraid.
>>>>>>>
>>>>>>> Markus Gschwind wrote:
>>>>>>>
>>>>>>> Dear Donald!
>>>>>>>
>>>>>>> That is a brilliant idea! Thanks, I have been waiting for this
>>>>>>> and it definitively facilitates work flow!
>>>>>>>
>>>>>>> However when ./build, I get the following error on MacOSX Snow
>>>>>>> Leopard:
>>>>>>>
>>>>>>> Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ ./build
>>>>>>> [CC] cmd/dir2amp.o
>>>>>>> [CC] cmd/streamtrack.o
>>>>>>> [CC] cmd/gen_unit_warp.o
>>>>>>> [CC] src/dwi/tractography/tracker/sd_prob.o
>>>>>>> [CC] cmd/import_tracks.o
>>>>>>> [CC] src/dwi/tractography/tracker/base.o
>>>>>>> [CC] src/mrview/sidebar/orientation_plot.o
>>>>>>> [CC] cmd/mrabs.o
>>>>>>> [CC] src/mrview/sidebar/overlay.o
>>>>>>> [CC] src/mrview/dialog/opengl.o
>>>>>>> [CC] cmd/gendir.o
>>>>>>> [CC] src/mrview/sidebar/screen_capture.o
>>>>>>> [CC] src/dwi/tractography/file.o
>>>>>>> [CC] src/dwi/SH.o
>>>>>>> [CC] cmd/tensor2ADC.o
>>>>>>> [CC] lib/image/format/mri.o
>>>>>>> [CC] cmd/dwi2tensor.o
>>>>>>> [CC] src/mrview/sidebar/tractography.o
>>>>>>> [CC] src/mrview/display_area.o
>>>>>>> [CC] src/mrview/image.o
>>>>>>> [CC] src/mrview/mode/base.o
>>>>>>> [CC] lib/image/format/list.o
>>>>>>> [CC] lib/image/format/xds.o
>>>>>>> [CC] src/histogram.o
>>>>>>> [CC] src/mrview/sidebar/tractography/track_list.o
>>>>>>> [CC] src/mrview/slice.o
>>>>>>> [CC] cmd/disp_profile.o
>>>>>>> [CC] lib/file/dicom/mapper.o
>>>>>>> [CC] cmd/resample_tracks.o
>>>>>>> [CC] cmd/tracks2prob.o
>>>>>>> [CC] lib/image/object.o
>>>>>>> [CC] src/mrview/dialog/error.o
>>>>>>> [CC] cmd/dwi2SH.o
>>>>>>> [CC] cmd/mrtransform.o
>>>>>>> [CC] cmd/gen_ROI.o
>>>>>>> [CC] cmd/csdeconv.o
>>>>>>> [CC] cmd/mradd.o
>>>>>>> [CC] cmd/sample_tracks.o
>>>>>>> [CC] src/dwi/tractography/tracker/dt_stream.o
>>>>>>> [CC] src/min_max.o
>>>>>>> [CC] cmd/erode.o
>>>>>>> [CC] cmd/filter_tracks.o
>>>>>>> [CC] cmd/mrcat.o
>>>>>>> [CC] src/mrview/sidebar/tractography/roi_list.o
>>>>>>> [CC] lib/image/interp.o
>>>>>>> [CC] lib/image/format/nifti1.o
>>>>>>> [CC] cmd/sdeconv.o
>>>>>>> [CC] lib/image/format/analyse.o
>>>>>>> [CC] lib/image/mapper.o
>>>>>>> [CC] cmd/read_ximg.o
>>>>>>> [CC] cmd/gen_WM_mask.o
>>>>>>> [CC] cmd/tensor_metric.o
>>>>>>> [CC] lib/image/fft.o
>>>>>>> [CC] cmd/mrmult.o
>>>>>>> [CC] src/mrview/sidebar/main.o
>>>>>>> [CC] cmd/normalise_tracks.o
>>>>>>> [CC] cmd/mrinfo.o
>>>>>>> [CC] cmd/mrconvert.o
>>>>>>> [CC] cmd/dicom_filename.o
>>>>>>> [CC] cmd/tensor2FA.o
>>>>>>> [CC] cmd/track_info.o
>>>>>>> [CC] cmd/truncate_tracks.o
>>>>>>> [CC] lib/mrtrix.o
>>>>>>> [CC] src/mrview/window.o
>>>>>>> [CC] src/mrview/sidebar/roi_analysis.o
>>>>>>> [CC] cmd/tracks2vtk.o
>>>>>>> [CC] src/mrview/pane.o
>>>>>>> [CC] lib/args.o
>>>>>>> [CC] src/dialog/file.o
>>>>>>> [CC] cmd/threshold.o
>>>>>>> [CC] lib/app.o
>>>>>>> [CC] src/mrview/mode/normal.o
>>>>>>> [CC] cmd/median3D.o
>>>>>>> [CC] src/mrview/sidebar/tractography/track_list_item.o
>>>>>>> [CC] cmd/estimate_response.o
>>>>>>> [CC] cmd/select_tracks.o
>>>>>>> [CC] cmd/read_dicom.o
>>>>>>> [CC] cmd/mrview.o
>>>>>>> [CC] cmd/find_SH_peaks.o
>>>>>>> [CC] cmd/mrstats.o
>>>>>>> [CC] cmd/average.o
>>>>>>> [CC] src/dwi/tractography/mds.o
>>>>>>> [CC] src/mrview/dialog/properties.o
>>>>>>> [CC] src/mrview/sidebar/roi_analysis/roi_list.o
>>>>>>> [CC] cmd/tensor2vector.o
>>>>>>> [CC] lib/image/format/mrtrix.o
>>>>>>> [CC] src/dwi/tractography/tracker/sd_stream.o
>>>>>>> [CC] lib/image/format/dicom.o
>>>>>>> [LD] lib/libmrtrix-0_2_10.dylib
>>>>>>>
>>>>>>>
>>>>>>> ERROR: [LD] lib/libmrtrix-0_2_10.dylib
>>>>>>>
>>>>>>> g++ -shared lib/math/vector.o lib/math/matrix.o
>>>>>>> lib/image/format/analyse.o lib/file/dicom/quick_scan.o
>>>>>>> lib/image/format/list.o lib/file/dicom/image.o lib/file/config.o
>>>>>>> lib/point.o lib/image/name_parser.o lib/image/format/xds.o lib/data_type.o
>>>>>>> lib/args.o lib/file/dicom/patient.o lib/file/dicom/tree.o lib/image/fft.o
>>>>>>> lib/image/header.o lib/file/dicom/mapper.o lib/file/dicom/select_cmdline.o
>>>>>>> lib/math/linalg.o lib/file/dicom/study.o lib/file/dicom/element.o
>>>>>>> lib/file/mmap.o lib/image/format/nifti1.o lib/file/dicom/dict.o
>>>>>>> lib/image/format/mrtrix.o lib/image/format/base.o lib/image/axis.o
>>>>>>> lib/image/interp.o lib/image/mapper.o lib/file/dicom/series.o lib/mrtrix.o
>>>>>>> lib/image/format/mri.o lib/image/object.o lib/image/format/dicom.o
>>>>>>> lib/app.o lib/file/key_value.o -L/usr/local/Cellar/glibmm/2.22.2/lib
>>>>>>> -L/usr/local/Cellar/glib/2.28.8/lib
>>>>>>> -L/usr/local/Cellar/libsigc++/2.2.10/lib -L/usr/local/Cellar/gettext/
>>>>>>> 0.18.1.1/lib -lglibmm-2.4 -lgobject-2.0 -lsigc-2.0 -lgthread-2.0
>>>>>>> -lglib-2.0 -lintl -lgsl -lgslcblas -o lib/libmrtrix-0_2_10.dylib
>>>>>>>
>>>>>>> failed with output:
>>>>>>>
>>>>>>> Undefined symbols for architecture x86_64:
>>>>>>> "_gzopen", referenced from:
>>>>>>> MR::Image::Mapper::gunzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&, char const*)in
>>>>>>> mapper.o
>>>>>>> "_gzread", referenced from:
>>>>>>> MR::Image::Mapper::gunzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&, char const*)in
>>>>>>> mapper.o
>>>>>>> "_gzclose", referenced from:
>>>>>>> MR::Image::Mapper::gunzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&, char const*)in
>>>>>>> mapper.o
>>>>>>> MR::Image::Mapper::gzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&,
>>>>>>> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>>>>>>> const&)in mapper.o
>>>>>>> "_gzdopen", referenced from:
>>>>>>> MR::Image::Mapper::gzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&,
>>>>>>> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>>>>>>> const&)in mapper.o
>>>>>>> "_gzwrite", referenced from:
>>>>>>> MR::Image::Mapper::gzip(std::basic_string<char,
>>>>>>> std::char_traits<char>, std::allocator<char> > const&,
>>>>>>> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>>>>>>> const&)in mapper.o
>>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>>> collect2: ld returned 1 exit status
>>>>>>>
>>>>>>>
>>>>>>> the following ./build install
>>>>>>> gives an error too:
>>>>>>>
>>>>>>> Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ sudo ./build
>>>>>>> install
>>>>>>> Password:
>>>>>>> installing executables to "/usr/local/mrtrix/bin" and dynamic
>>>>>>> library to "/usr/local/mrtrix/lib"...
>>>>>>> Traceback (most recent call last):
>>>>>>> File "./build", line 914, in <module>
>>>>>>> apply_recursive (install, os.path.join (lib_dir, libname),
>>>>>>> os.path.join (dest_lib, libname))
>>>>>>> File "./build", line 736, in apply_recursive
>>>>>>> action (source, destination)
>>>>>>> File "./build", line 753, in install
>>>>>>> shutil.copy (source, destination)
>>>>>>> File
>>>>>>> "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/shutil.py",
>>>>>>> line 88, in copy
>>>>>>> copyfile(src, dst)
>>>>>>> File
>>>>>>> "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/shutil.py",
>>>>>>> line 52, in copyfile
>>>>>>> fsrc = open(src, 'rb')
>>>>>>> IOError: [Errno 2] No such file or directory:
>>>>>>> 'lib/libmrtrix-0_2_10.dylib'
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> What should I do to make it work?
>>>>>>>
>>>>>>> Thanks in advance!
>>>>>>> Best wishes,
>>>>>>> Markus
>>>>>>>
>>>>>>> 2012/3/5 Donald Tournier <d.tournier at brain.org.au>
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> Many of you may be interested in being able to read & write
>>>>>>>> compressed NIfTI images (.nii.gz) directly within MRtrix. Here is a patch
>>>>>>>> to do just this, and to also read/write compressed MRtrix format (.mif.gz),
>>>>>>>> thanks to Chris Adamson (unfortunately just too late for the last release).
>>>>>>>> This patch is to be applied to the current 0.2.10 release version, with the
>>>>>>>> following instructions (edit as appropriate):
>>>>>>>>
>>>>>>>> $ cd mrtrix-0.2.10
>>>>>>>> $ tar xvfj mrtrix-patch-GZ.tar.bz2
>>>>>>>> $ ./build
>>>>>>>> $ sudo ./build install
>>>>>>>>
>>>>>>>> Note that this patch hasn't been thoroughly tested, although it
>>>>>>>> seems to work fine. It's also only been tested on Linux, so may or may not
>>>>>>>> work on other platforms - if anyone is willing to try it out, I'd be
>>>>>>>> interested to hear about it.
>>>>>>>>
>>>>>>>> Hope this proves useful!
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Donald
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Jacques-Donald Tournier (PhD)
>>>>>>>> Brain Research Institute, Melbourne, Australia
>>>>>>>> Tel: +61 (0)3 9035 7033
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Mrtrix-discussion mailing list
>>>>>>>> Mrtrix-discussion at www.nitrc.org
>>>>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -
>>>>>>>
>>>>>>> ------------------------------
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Mrtrix-discussion mailing listMrtrix-discussion at www.nitrc.orghttp://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Jacques-Donald Tournier (PhD)
>>>>>> Brain Research Institute, Melbourne, Australia
>>>>>> Tel: +61 (0)3 9035 7033
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Jacques-Donald Tournier (PhD)
>>>> Brain Research Institute, Melbourne, Australia
>>>> Tel: +61 (0)3 9035 7033
>>>>
>>>
>>>
>>>
>>> --
>>>
>>
>>
>>
>> --
>>
>>
>
>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
>
--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition - Dept of Neurosciences
University Medical Center (CMU)
1, Michel-Servet
CH-1211 GENEVA - Switzerland
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: markus.gschwind at unige.ch
http://labnic.unige.ch
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