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

Donald Tournier d.tournier at brain.org.au
Wed Mar 7 19:56:56 PST 2012 

Hi Markus,

Just to follow up on that: I've just done a bit more testing, and as far as
I can tell everything works perfectly on my Snow Leopard install. So if
you're still having issues, best thing would be to post that command-line
session as I suggested in my previous email.

Cheers,

Donald.


On 7 March 2012 17:48, Donald Tournier <d.tournier at brain.org.au> wrote:

> Hi Markus,
>
> I had a go at installing the patch on a Snow Leopard machine here, and it
> seems to mostly work OK for me. I did have an issue writing back a
> compressed MRtrix (.mif) file, which I'll investigate further when I have a
> minute, but otherwise it seemed to load compressed nifti files OK...
>
> Maybe you could post the entire command-line session from extraction of
> the original MRtrix install, through the patching process, building and
> install, up to running a failing command? I'm really struggling to see how
> the code could report an unknown format, and given that this aspect works
> fine on a system here, I just want to rule out any other issues first.
>
> Cheers,
>
> Donald.
>
>
> On 7 March 2012 16:57, Markus Gschwind <markus.gschwind at gmail.com> wrote:
>
>> 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
>>>
>>
>>
>>
>>
>>
>
>
> --
> 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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