[Mrtrix-discussion] support for MIF & NIfTI GZ compression

[Markus Gschwind]

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
>
>


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