Hi Markus,<div><br></div><div>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...</div>
<div><br></div><div>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.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br><br><div class="gmail_quote">On 7 March 2012 16:57, Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com">markus.gschwind@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Donald,<div><br></div><div>I think I did a complete new reinstall, and then added the new patch.</div><div><br></div>
<div>The -version option gives this:</div><div><br></div><div>MacBook Pro$ mrview -version</div><div>
<div>mrview 0.2.10 (revision 327)</div><div> Author: J-Donald Tournier (<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>)</div><div> Copyright 2008 Brain Research Institute, Melbourne, Australia</div>
<div> using MRtrix 0.2.10, glib 2.28.8, GSL 1.15 (build Mar 5 2012)</div><div><br></div><div><br></div><div>And here is the -debug option</div><div><br></div><div><div>$ mrinfo -debug CONT_dti_FA_space_bin.nii.gz </div>
<div>mrinfo [DEBUG]: reading key/value file "/etc/mrtrix.conf"...</div><div>mrinfo [INFO]: opening image "CONT_dti_FA_space_bin.nii.gz"...</div><div class="im"><div>mrinfo: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"</div>
<div>mrinfo: error opening image "CONT_dti_FA_space_bin.nii.gz"</div></div><div>mrinfo [INFO]: closing image "CONT_dti_FA_space_bin.nii.gz"...</div></div><div><br></div><div><br></div><div><div>$ mrview -info -debug CONT_dti_FA_space_bin.nii.gz </div>
<div>mrview [DEBUG]: reading key/value file "/etc/mrtrix.conf"...</div><div><br></div><div>(process:3026): Gtk-WARNING **: Locale not supported by C library.</div><div class="im"><div><span style="white-space:pre-wrap"> </span>Using the fallback 'C' locale.</div>
<div>Xlib: extension "RANDR" missing on display "/tmp/launch-29bcMY/org.x:0".</div></div><div>mrview [INFO]: opening image "CONT_dti_FA_space_bin.nii.gz"...</div><div class="im"><div>mrview: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"</div>
<div>mrview: error opening image "CONT_dti_FA_space_bin.nii.gz"</div></div><div>mrview [INFO]: closing image "CONT_dti_FA_space_bin.nii.gz"...</div></div><div><br></div><div><br></div><div>Thanks for your help!!</div>
<div><div class="h5">
<div>Markus</div><br><div class="gmail_quote">2012/3/6 Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Markus,<div><br></div><div>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: <a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-February/000369.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2012-February/000369.html</a> ? 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...</div>
<div><br></div><div>Cheers,</div><div><br></div><font color="#888888"><div>Donald.</div></font><div><div></div><div><div><br></div><div><br><div class="gmail_quote">On 7 March 2012 08:39, Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com" target="_blank">markus.gschwind@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all!<div><br></div><div>Thanks for the help in debugging!</div><div><br></div><div>I have now installed the new patch of Donald.</div>
<div><br></div><div><div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ tar xvfj mrtrix-patch-GZ.tar.bz2 </div>
<div>x build</div><div>x lib/image/format/list.cpp</div><div>x lib/image/format/mrtrix.cpp</div><div>x lib/image/format/nifti1.cpp</div><div>x lib/image/mapper.cpp</div><div>x lib/image/mapper.h</div><div>x lib/image/object.cpp</div>
<div>x lib/image/object.h</div><div>x sysconf/linux.py</div><div>x sysconf/darwin.py</div><div>x sysconf/windows.py</div><div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ ./build</div><div><div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ sudo ./build install</div>
</div><div>installing executables to "/usr/local/mrtrix/bin" and dynamic library to "/usr/local/mrtrix/lib"... ok</div><div>creating symbolic links to executables in "/usr/local/bin" and to dynamic library in "/usr/local/lib"... ok</div>
<div>configuration file already exists - leaving as-is</div><div>Markus-Gschwinds-MacBook-Pro:mrtrix-0.2.10 markus$ </div></div><div><br></div><div><br></div><div><br></div><div>However, there seems still to be a problem:</div>
<div><br></div><div><div>Markus-Gschwinds-MacBook-Pro:CONT markus$ mrinfo CONT_dti_FA_space_bin.nii.gz </div><div>mrinfo: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"</div><div>mrinfo: error opening image "CONT_dti_FA_space_bin.nii.gz"</div>
</div><div><br></div><div><br></div><div><br></div><div><div>Markus-Gschwinds-MacBook-Pro:CONT markus$ mrview CONT_dti_FA_space_bin.nii.gz </div><div><br></div><div>(process:377): Gtk-WARNING **: Locale not supported by C library.</div>
<div><span style="white-space:pre-wrap"> </span>Using the fallback 'C' locale.</div><div>Xlib: extension "RANDR" missing on display "/tmp/launch-29bcMY/org.x:0".</div><div>mrview: unknown format for image "./CONT_dti_FA_space_bin.nii.gz"</div>
<div>mrview: error opening image "CONT_dti_FA_space_bin.nii.gz"</div><div><br></div><div><br></div><div>Thanks!</div><span><font color="#888888"><div><br></div><div>Markus</div></font></span><div>
<div><div><br></div><br><div class="gmail_quote">2012/3/6 Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Markus,<div><br></div><div>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:<br>
<br><div> '$obj$': [ item for item in self.deps ] + pkg (pkgconfig_glib, 'libs') + ld_flags_gsl + ld_flags_zlib,</div><div><br></div><div>(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...</div>
<div><br></div><div>Cheers,</div><div><br></div><font color="#888888"><div>Donald.</div></font><div><div></div><div><div><br></div><br><div class="gmail_quote">On 6 March 2012 21:59, Ian Malone <span dir="ltr"><<a href="mailto:i.malone@ucl.ac.uk" target="_blank">i.malone@ucl.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div bgcolor="#ffffff" text="#000000">
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 type="cite"><div><div>
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 href="http://0.18.1.1/lib" target="_blank">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 href="mailto:d.tournier@brain.org.au" target="_blank">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 href="tel:%2B61%20%280%293%209035%207033" value="+61390357033" target="_blank">+61 (0)3 9035 7033</a><br>
</font></div>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-<br>
</div>
</div></div><pre><hr size="4" width="90%"><div>
_______________________________________________
Mrtrix-discussion mailing list
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<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a>
</div></pre>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: <a href="tel:%2B61%20%280%293%209035%207033" value="+61390357033" target="_blank">+61 (0)3 9035 7033</a><br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div><br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: <a href="tel:%2B61%20%280%293%209035%207033" value="+61390357033" target="_blank">+61 (0)3 9035 7033</a><br>
</div>
</div></div></blockquote></div><br><br clear="all"><div><br></div><br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>
</div>