[Mrtrix-discussion] support for MIF & NIfTI GZ compression
Markus Gschwind
markus.gschwind at gmail.com
Tue Mar 6 13:39:26 PST 2012
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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20120306/eb7e57da/attachment.html
More information about the Mrtrix-discussion
mailing list