[Mrtrix-discussion] support for MIF & NIfTI GZ compression
Ian Malone
i.malone at ucl.ac.uk
Tue Mar 6 02:59:52 PST 2012
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 <http://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
> <mailto: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 <tel:%2B61%20%280%293%209035%207033>
>
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>
>
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