[Mrtrix-discussion] support for MIF & NIfTI GZ compression
Donald Tournier
d.tournier at brain.org.au
Tue Mar 6 14:53:22 PST 2012
Hi Markus,
Glad to hear it compiled OK on the mac. Your remaining issue is a bit
unexpected though. Are you sure you're running the latest version? What
does 'mrconvert -version' report? Maybe you're having a similar issue to
this one:
http://www.nitrc.org/pipermail/mrtrix-discussion/2012-February/000369.html ?
If not, then I'm a bit puzzled. Maybe running the command with the -debug
option would give a bit more information to try to figure out what is going
on...
Cheers,
Donald.
On 7 March 2012 08:39, Markus Gschwind <markus.gschwind at gmail.com> wrote:
> Dear all!
>
> Thanks for the help in debugging!
>
> I have now installed the new patch of Donald.
>
> 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$
>
>
>
> 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
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