[Mrtrix-discussion] Re: Mrtrix-discussion Digest, Vol 38, Issue 4
Chris Adamson
chris.adamson at mcri.edu.au
Tue Mar 6 03:04:28 PST 2012
I didn't add the zlib argument to the Mac os x config file. The second error is caused by the first, the library not being created. I will send a patch tomorrow.
On 06/03/2012, at 9:59 PM, "mrtrix-discussion-request at www.nitrc.org" <mrtrix-discussion-request at www.nitrc.org> wrote:
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> Today's Topics:
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> 1. Re: support for MIF & NIfTI GZ compression (Markus Gschwind)
> 2. Re: support for MIF & NIfTI GZ compression (Ian Malone)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Mar 2012 22:07:56 +0100
> From: Markus Gschwind <markus.gschwind at gmail.com>
> Subject: Re: [Mrtrix-discussion] support for MIF & NIfTI GZ
> compression
> To: Donald Tournier <d.tournier at brain.org.au>
> Cc: mrtrix-discussion at www.nitrc.org
> Message-ID:
> <CABaUQnxnGUX4cs1J3mZg1g_G5X4nNWLO=izpCuLXUnPejVgWug at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
>>
>>
>
>
> -
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 6 Mar 2012 10:59:52 +0000
> From: Ian Malone <i.malone at ucl.ac.uk>
> Subject: Re: [Mrtrix-discussion] support for MIF & NIfTI GZ
> compression
> To: Markus Gschwind <markus.gschwind at gmail.com>
> Cc: mrtrix-discussion at www.nitrc.org
> Message-ID: <4F55EE28.8000500 at ucl.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> <mailto:Mrtrix-discussion at www.nitrc.org>
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>>
>>
>> -
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>
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>
> End of Mrtrix-discussion Digest, Vol 38, Issue 4
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