Hi Nick,
I tried running mri_watershed on Anthony's computer today and got a different error from last time. I got the following error:
% freesurfer/bin/mri_watershed dyld: freesurfer/bin/mri_watershed can't open library: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (No such file or directory, errno = 2) Trace/BPT trap
So I installed gsl and gsl-shlibs, and I've gotten mri_watershed to work for me. I will have Anthony and then another user try it out to see if installing gsl fixed the issue and let you know. Thank you.
Xander
On Apr 4, 2006, at 4:05 PM, Nick Schmansky wrote:
Anthony,
I don't know what to recommend. I cannot seem to find this symbol defined anywhere (even Googling it). The panther distribution has worked for two other people (that i know of) outside of MGH, so I'm not sure what I can suggest. The 'otool' output looks correct.
If I can think of any other debugging techniques to try, I will send them along.
Nick
On Mon, 2006-04-03 at 14:06 -0500, Anthony Steven Dick wrote:
Hi Nick--
I'm responding on behalf of Xander (our computer tech):
[serge:NL-GCS/subjects/freesurfer_3.0.1] adick% otool -L `which mri_watershed`
/Applications/freesurfer/bin//mri_watershed:
/usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (compatibility version 8.0.0, current version 8.0.0) /usr/pubsw/packages/gsl/current/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.5) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0)
Anthony
Nick Schmansky wrote:
Can you send me the output of:
otool -L `which mri_watershed`
On Mon, 2006-04-03 at 13:34 -0500, xmeadow@uchicago.edu wrote:
Hi,
I just downloaded and installed from:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin- panther- stable-pub-v3.0.1-full.dmg
And installed Freesurfer. Most of the apps have worked without a problem, however mri_watershed yields the following error:
dyld: mri_watershed Undefined symbols: _acns Trace/BPT trap
I have redowndloaded the above package and tried to extract mri_watershed, in case I just got a corrupted binary, but each time I do so I get the same errors. My machine is running MAC OS X 10.3.9. Please let me know if there is any fix I can do for this error? Thank you very much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
Just wanted to let you know that Anthony has tried mri_watershed and after installing the gsl binary everything seems to work fine. Thank you for everything.
Xander
On Apr 4, 2006, at 4:25 PM, Xander Meadow wrote:
Hi Nick,
I tried running mri_watershed on Anthony's computer today and got a different error from last time. I got the following error:
% freesurfer/bin/mri_watershed dyld: freesurfer/bin/mri_watershed can't open library: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (No such file or directory, errno = 2) Trace/BPT trap
So I installed gsl and gsl-shlibs, and I've gotten mri_watershed to work for me. I will have Anthony and then another user try it out to see if installing gsl fixed the issue and let you know. Thank you.
Xander
On Apr 4, 2006, at 4:05 PM, Nick Schmansky wrote:
Anthony,
I don't know what to recommend. I cannot seem to find this symbol defined anywhere (even Googling it). The panther distribution has worked for two other people (that i know of) outside of MGH, so I'm not sure what I can suggest. The 'otool' output looks correct.
If I can think of any other debugging techniques to try, I will send them along.
Nick
On Mon, 2006-04-03 at 14:06 -0500, Anthony Steven Dick wrote:
Hi Nick--
I'm responding on behalf of Xander (our computer tech):
[serge:NL-GCS/subjects/freesurfer_3.0.1] adick% otool -L `which mri_watershed`
/Applications/freesurfer/bin//mri_watershed:
/usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (compatibility version 8.0.0, current version 8.0.0) /usr/pubsw/packages/gsl/current/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.5) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0)
Anthony
Nick Schmansky wrote:
Can you send me the output of:
otool -L `which mri_watershed`
On Mon, 2006-04-03 at 13:34 -0500, xmeadow@uchicago.edu wrote:
Hi,
I just downloaded and installed from:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin- panther- stable-pub-v3.0.1-full.dmg
And installed Freesurfer. Most of the apps have worked without a problem, however mri_watershed yields the following error:
dyld: mri_watershed Undefined symbols: _acns Trace/BPT trap
I have redowndloaded the above package and tried to extract mri_watershed, in case I just got a corrupted binary, but each time I do so I get the same errors. My machine is running MAC OS X 10.3.9. Please let me know if there is any fix I can do for this error? Thank you very much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Xander,
I'm glad its working for you. I'm not sure why it did not work as-is, because the GSL library is included with the distribution (in $FREESURFER_HOME/lib/gsl) and the DYLD_LIBRARY_PATH is setup to point to it. I do need to figure-out why the hard-coded path '/usr/pubsw/packages' is shown by otool, but if its working now, then good.
Nick
On Wed, 2006-04-05 at 09:17 -0500, Xander Meadow wrote:
Hi Nick,
Just wanted to let you know that Anthony has tried mri_watershed and after installing the gsl binary everything seems to work fine. Thank you for everything.
Xander
On Apr 4, 2006, at 4:25 PM, Xander Meadow wrote:
Hi Nick, I tried running mri_watershed on Anthony's computer today and got a different error from last time. I got the following error: % freesurfer/bin/mri_watershed dyld: freesurfer/bin/mri_watershed can't open library: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (No such file or directory, errno = 2) Trace/BPT trap So I installed gsl and gsl-shlibs, and I've gotten mri_watershed to work for me. I will have Anthony and then another user try it out to see if installing gsl fixed the issue and let you know. Thank you. >Xander On Apr 4, 2006, at 4:05 PM, Nick Schmansky wrote: Anthony, I don't know what to recommend. I cannot seem to find this symbol defined anywhere (even Googling it). The panther distribution has worked for two other people (that i know of) outside of MGH, so I'm not sure what I can suggest. The 'otool' output looks correct. If I can think of any other debugging techniques to try, I will send them along. Nick On Mon, 2006-04-03 at 14:06 -0500, Anthony Steven Dick wrote: Hi Nick-- I'm responding on behalf of Xander (our computer tech): [serge:NL-GCS/subjects/freesurfer_3.0.1] adick % otool -L `which mri_watershed` /Applications/freesurfer/bin//mri_watershed: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (compatibility version 8.0.0, current version 8.0.0) /usr/pubsw/packages/gsl/current/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.5) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0) Anthony Nick Schmansky wrote: Can you send me the output of: otool -L `which mri_watershed` On Mon, 2006-04-03 at 13:34 -0500, xmeadow@uchicago.edu wrote: Hi, I just downloaded and installed from: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-panther- stable-pub-v3.0.1-full.dmg And installed Freesurfer. Most of the apps have worked without a problem, however mri_watershed yields the following error: dyld: mri_watershed Undefined symbols: _acns Trace/BPT trap I have redowndloaded the above package and tried to extract mri_watershed, in case I just got a corrupted binary, but each time I do so I get the same errors. My machine is running MAC OS X 10.3.9. Please let me know if there is any fix I can do for this error? Thank you very much. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Xander Meadow