[Mrtrix-discussion] support for MIF & NIfTI GZ compression
Markus Gschwind
markus.gschwind at gmail.com
Tue Mar 6 21:57:08 PST 2012
Dear Donald,
I think I did a complete new reinstall, and then added the new patch.
The -version option gives this:
MacBook Pro$ mrview -version
mrview 0.2.10 (revision 327)
Author: J-Donald Tournier (d.tournier at brain.org.au)
Copyright 2008 Brain Research Institute, Melbourne, Australia
using MRtrix 0.2.10, glib 2.28.8, GSL 1.15 (build Mar 5 2012)
And here is the -debug option
$ mrinfo -debug CONT_dti_FA_space_bin.nii.gz
mrinfo [DEBUG]: reading key/value file "/etc/mrtrix.conf"...
mrinfo [INFO]: opening image "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"
mrinfo [INFO]: closing image "CONT_dti_FA_space_bin.nii.gz"...
$ mrview -info -debug CONT_dti_FA_space_bin.nii.gz
mrview [DEBUG]: reading key/value file "/etc/mrtrix.conf"...
(process:3026): 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 [INFO]: opening image "CONT_dti_FA_space_bin.nii.gz"...
mrview: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"
mrview: error opening image "CONT_dti_FA_space_bin.nii.gz"
mrview [INFO]: closing image "CONT_dti_FA_space_bin.nii.gz"...
Thanks for your help!!
Markus
2012/3/6 Donald Tournier <d.tournier at brain.org.au>
> 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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