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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.<br>
<br>
Markus Gschwind wrote:
<blockquote
cite="mid:CABaUQnxnGUX4cs1J3mZg1g_G5X4nNWLO=izpCuLXUnPejVgWug@mail.gmail.com"
type="cite">
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Dear Donald!
<div><br>
</div>
<div>That is a brilliant idea! Thanks, I have been waiting for this
and it definitively facilitates work flow!</div>
<div><br>
</div>
<div>However when ./build, I get the following error on MacOSX Snow
Leopard:</div>
<div><br>
</div>
<div>
<div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ ./build</div>
<div>[CC] cmd/dir2amp.o</div>
<div>[CC] cmd/streamtrack.o</div>
<div>[CC] cmd/gen_unit_warp.o</div>
<div>[CC] src/dwi/tractography/tracker/sd_prob.o</div>
<div>[CC] cmd/import_tracks.o</div>
<div>[CC] src/dwi/tractography/tracker/base.o</div>
<div>[CC] src/mrview/sidebar/orientation_plot.o</div>
<div>[CC] cmd/mrabs.o</div>
<div>[CC] src/mrview/sidebar/overlay.o</div>
<div>[CC] src/mrview/dialog/opengl.o</div>
<div>[CC] cmd/gendir.o</div>
<div>[CC] src/mrview/sidebar/screen_capture.o</div>
<div>[CC] src/dwi/tractography/file.o</div>
<div>[CC] src/dwi/SH.o</div>
<div>[CC] cmd/tensor2ADC.o</div>
<div>[CC] lib/image/format/mri.o</div>
<div>
[CC] cmd/dwi2tensor.o</div>
<div>[CC] src/mrview/sidebar/tractography.o</div>
<div>[CC] src/mrview/display_area.o</div>
<div>[CC] src/mrview/image.o</div>
<div>[CC] src/mrview/mode/base.o</div>
<div>[CC] lib/image/format/list.o</div>
<div>[CC] lib/image/format/xds.o</div>
<div>[CC] src/histogram.o</div>
<div>[CC] src/mrview/sidebar/tractography/track_list.o</div>
<div>[CC] src/mrview/slice.o</div>
<div>[CC] cmd/disp_profile.o</div>
<div>[CC] lib/file/dicom/mapper.o</div>
<div>[CC] cmd/resample_tracks.o</div>
<div>[CC] cmd/tracks2prob.o</div>
<div>[CC] lib/image/object.o</div>
<div>[CC] src/mrview/dialog/error.o</div>
<div>[CC] cmd/dwi2SH.o</div>
<div>[CC] cmd/mrtransform.o</div>
<div>[CC] cmd/gen_ROI.o</div>
<div>[CC] cmd/csdeconv.o</div>
<div>[CC] cmd/mradd.o</div>
<div>[CC] cmd/sample_tracks.o</div>
<div>[CC] src/dwi/tractography/tracker/dt_stream.o</div>
<div>[CC] src/min_max.o</div>
<div>[CC] cmd/erode.o</div>
<div>[CC] cmd/filter_tracks.o</div>
<div>[CC] cmd/mrcat.o</div>
<div>[CC] src/mrview/sidebar/tractography/roi_list.o</div>
<div>[CC] lib/image/interp.o</div>
<div>[CC] lib/image/format/nifti1.o</div>
<div>[CC] cmd/sdeconv.o</div>
<div>[CC] lib/image/format/analyse.o</div>
<div>[CC] lib/image/mapper.o</div>
<div>[CC] cmd/read_ximg.o</div>
<div>[CC] cmd/gen_WM_mask.o</div>
<div>[CC] cmd/tensor_metric.o</div>
<div>[CC] lib/image/fft.o</div>
<div>[CC] cmd/mrmult.o</div>
<div>[CC] src/mrview/sidebar/main.o</div>
<div>[CC] cmd/normalise_tracks.o</div>
<div>[CC] cmd/mrinfo.o</div>
<div>[CC] cmd/mrconvert.o</div>
<div>[CC] cmd/dicom_filename.o</div>
<div>[CC] cmd/tensor2FA.o</div>
<div>[CC] cmd/track_info.o</div>
<div>[CC] cmd/truncate_tracks.o</div>
<div>[CC] lib/mrtrix.o</div>
<div>[CC] src/mrview/window.o</div>
<div>[CC] src/mrview/sidebar/roi_analysis.o</div>
<div>[CC] cmd/tracks2vtk.o</div>
<div>[CC] src/mrview/pane.o</div>
<div>[CC] lib/args.o</div>
<div>[CC] src/dialog/file.o</div>
<div>[CC] cmd/threshold.o</div>
<div>[CC] lib/app.o</div>
<div>[CC] src/mrview/mode/normal.o</div>
<div>[CC] cmd/median3D.o</div>
<div>[CC] src/mrview/sidebar/tractography/track_list_item.o</div>
<div>[CC] cmd/estimate_response.o</div>
<div>[CC] cmd/select_tracks.o</div>
<div>[CC] cmd/read_dicom.o</div>
<div>[CC] cmd/mrview.o</div>
<div>[CC] cmd/find_SH_peaks.o</div>
<div>[CC] cmd/mrstats.o</div>
<div>[CC] cmd/average.o</div>
<div>[CC] src/dwi/tractography/mds.o</div>
<div>[CC] src/mrview/dialog/properties.o</div>
<div>[CC] src/mrview/sidebar/roi_analysis/roi_list.o</div>
<div>[CC] cmd/tensor2vector.o</div>
<div>[CC] lib/image/format/mrtrix.o</div>
<div>[CC] src/dwi/tractography/tracker/sd_stream.o</div>
<div>[CC] lib/image/format/dicom.o</div>
<div>[LD] lib/libmrtrix-0_2_10.dylib</div>
<div><br>
</div>
</div>
<div><br>
</div>
<div>
<div>ERROR: [LD] lib/libmrtrix-0_2_10.dylib</div>
<div><br>
</div>
<div>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/<a
moz-do-not-send="true" href="http://0.18.1.1/lib">0.18.1.1/lib</a>
-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</div>
<div><br>
</div>
<div>failed with output:</div>
<div><br>
</div>
<div>Undefined symbols for architecture x86_64:</div>
<div> "_gzopen", referenced from:</div>
<div> MR::Image::Mapper::gunzip(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >
const&, char const*)in mapper.o</div>
<div> "_gzread", referenced from:</div>
<div> MR::Image::Mapper::gunzip(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >
const&, char const*)in mapper.o</div>
<div> "_gzclose", referenced from:</div>
<div> MR::Image::Mapper::gunzip(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >
const&, char const*)in mapper.o</div>
<div> 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</div>
<div> "_gzdopen", referenced from:</div>
<div> 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</div>
<div> "_gzwrite", referenced from:</div>
<div> 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</div>
<div>ld: symbol(s) not found for architecture x86_64</div>
<div>collect2: ld returned 1 exit status</div>
<div><br>
</div>
<div><br>
</div>
<div>the following ./build install </div>
<div>gives an error too:</div>
<div><br>
</div>
<div>
<div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ sudo ./build
install</div>
<div>Password:</div>
<div>installing executables to "/usr/local/mrtrix/bin" and dynamic
library to "/usr/local/mrtrix/lib"...</div>
<div>Traceback (most recent call last):</div>
<div> File "./build", line 914, in <module></div>
<div> apply_recursive (install, os.path.join (lib_dir, libname),
os.path.join (dest_lib, libname))</div>
<div> File "./build", line 736, in apply_recursive</div>
<div> action (source, destination)</div>
<div> File "./build", line 753, in install</div>
<div> shutil.copy (source, destination)</div>
<div> File
"/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/shutil.py",
line 88, in copy</div>
<div> copyfile(src, dst)</div>
<div> File
"/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/shutil.py",
line 52, in copyfile</div>
<div> fsrc = open(src, 'rb')</div>
<div>IOError: [Errno 2] No such file or directory:
'lib/libmrtrix-0_2_10.dylib'</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>What should I do to make it work?</div>
<div><br>
</div>
<div>Thanks in advance!</div>
<div>Best wishes,</div>
<div>Markus</div>
<br>
<div class="gmail_quote">2012/3/5 Donald Tournier <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:d.tournier@brain.org.au">d.tournier@brain.org.au</a>></span><br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi
all,
<div><br>
</div>
<div>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):</div>
<div><br>
</div>
<div>$ cd mrtrix-0.2.10</div>
<div>$ tar xvfj mrtrix-patch-GZ.tar.bz2</div>
<div>$ ./build</div>
<div>$ sudo ./build install</div>
<div><br>
</div>
<div>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.
<div><br>
</div>
<div>Hope this proves useful!</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald</div>
<div><br>
</div>
<font color="#888888">
<div><br>
</div>
-- <br>
Jacques-Donald Tournier (PhD)<br>
Brain Research Institute, Melbourne, Australia<br>
Tel: <a moz-do-not-send="true"
href="tel:%2B61%20%280%293%209035%207033" value="+61390357033"
target="_blank">+61 (0)3 9035 7033</a><br>
</font></div>
<br>
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target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-<br>
</div>
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</blockquote>
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