malcolm, hi, i'm able to replicate that warning on that data, and i'm investigating. i would say its a false alarm, as that input data is considered 'optimal' (mprage from our own scanners).
it appears the recon-all proceeded successfully all the way to nearly the end. it failed in some new code (you are working with our 'development' checkout, so new stuff often breaks the stream), so i'll have to pass that failure along to that developer (thanks for catching that!). so i think your build seems fine. i notice you are running on a somewhat standard linux platform. does the centos binary build that we distribute not suit your needs? just wanted to make sure you werent under the impression that you have to build from scratch if you arent running centos (people have made assumption in the past). the centos build seems to run fine on nearly all x86 linux variants, sometimes with some library tweeking. its a help though to have developers such as yourself build the source. n. On Wed, 2012-01-11 at 07:53 -0600, Malcolm Tobias wrote: > Nick, > > I ran recon-all on bert and it did produce an error: > > recon-all -s ernie exited with ERRORS at Tue Jan 10 18:47:07 CST 2012 > > A cursory glance at the recon-all.log showed: > > ********************************************************** > * > * WARNING: Registration did not converge in 5 steps! > * Problem might be ill posed. > * Please inspect output manually! > * > ********************************************************** > > I'm not sure if that's the real problem or whether it occurs further down in > the logs. I've attached the entire log. > > Malcolm > > > On Tuesday 10 January 2012 10:58:21 Nick Schmansky wrote: > > malcolm, > > > > running 'make check' is one way to check the build. we run that nightly > > on our three build platforms (linux 32b, 64b and mac leopard). a goal > > of our linux centos build is to have it run on as many linux variants as > > possible without people having to modify their local install, and to > > that end, we've found that some linux systems dont have libg2c > > installed, so what we do on our build platforms is to remove the > > libg2c.so (shared lib) file, leaving the .a (static lib), so that the > > shared lib dependency is removed. you can either do the same (so far > > doing so hasnt broken other non-freesurfer apps), or you can skip it. > > > > you should run recon-all -all on 'bert', or any other data you have > > handy. make sure it runs to completion without error. checking the > > accuracy of the results against known prior runs is possible (we do this > > locally) but probably not necessary in your case, as your results might > > be different (due to platform differences) but not 'wrong'. mainly you > > want to make sure recon-all doesnt hit some strange runtime problem > > (missing lib or whatnot). remember you shouldn't mix results from your > > new platform with results from other platforms when conducting a group > > study (ie always do groups studies using results from the same platform > > and version). > > > > n > > > > On Tue, 2012-01-10 at 07:47 -0600, Malcolm Tobias wrote: > > > Nick, > > > > > > Everything is now building successfully. Thanks for your help! > > > > > > What do you normally do to test a build? I tried running 'make check' > > > which seemed pretty extensive. While many tests passed: > > > > > > [root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l > > > 407 > > > > > > I did have one fail: > > > > > > ERROR: gauss_4dfp built against shared libg2c! > > > FAIL: test_libg2c > > > > > > which seemed to stop the test process. Is this something serious or can > > > it be ignored? > > > > > > Malcolm > > > > > > On Monday 09 January 2012 15:43:34 Nick Schmansky wrote: > > > > malcolm, > > > > > > > > configure.in had another bug in it. attached is a fix. run > > > > setup_configure again to regenerate configure. its been awhile since > > > > someone built a non-gui build offsite, so there could be other > > > > problems. > > > > > > > > n. > > > > > > > > On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote: > > > > > Nick, > > > > > > > > > > While configure now works, I'm getting a build-time error. > > > > > > > > > > It looks like: > > > > > histo_register/SimpleBaseLib/include/sbl/image/Image.h > > > > > > > > > > has a dependency on OpenCV. I didn't see OpenCV listed on the > > > > > Developers Guide: > > > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide > > > > > > > > > > Is this a new dependency? > > > > > > > > > > I tried using "--without-opencv" but that generated an error with > > > > > freeview: > > > > > > > > > > make[2]: Entering directory > > > > > `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o > > > > > ui_MainWindow.h > > > > > make[2]: MainWindow.ui: Command not found > > > > > > > > > > Any suggestions? > > > > > > > > > > Malcolm > > > > > > > > > > On Monday 09 January 2012 13:36:37 Nick Schmansky wrote: > > > > > > malcolm, > > > > > > > > > > > > can you try using the attached configure.in? you will need to > > > > > > run ./setup_configure, which will create a new configure script. > > > > > > hopefully --disable-all-apps will then work. > > > > > > > > > > > > n. > > > > > > > > > > > > On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote: > > > > > > > Nick, > > > > > > > > > > > > > > I'm getting the same error: > > > > > > > > > > > > > > [root@login002 freesurfer-dev-20120106]# ./configure > > > > > > > --disable-all-apps -- disable-gl-apps --disable-tcltk-apps > > > > > > > -with-mni-dir=/export/minc-1.4/ --with- > > > > > > > vxl-dir=/export/vxl-1.13.0 ... > > > > > > > configure: error: FATAL: libBLT not found. Check config.log. Set > > > > > > > LDFLAGS or -- with-BLT-dir. > > > > > > > > > > > > > > I've attached the config.log. Let me know if the mail-list > > > > > > > software blocks it for any reason. > > > > > > > > > > > > > > Cheers, > > > > > > > Malcolm > > > > > > > > > > > > > > On Monday 09 January 2012 11:09:03 Nick Schmansky wrote: > > > > > > > > try addong --disable-tcltk-apps to your configure command > > > > > > > > line. > > > > > > > > > > > > > > > > --disable-all-apps appears to be broken. > > > > > > > > > > > > > > > > send me your config.log file if it still doesnt work. > > > > > > > > > > > > > > > > n. > > > > > > > > > > > > > > > > On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote: > > > > > > > > > Nick, > > > > > > > > > > > > > > > > > > Tcl/Tk is installed on the system under /usr/bin so I can't > > > > > > > > > exclude it from my path without breaking things. VTK isn't > > > > > > > > > in my path. > > > > > > > > > > > > > > > > > > Should the flags to disable the GUI stuff (--disable-all-apps > > > > > > > > > --disable-gl- apps) be considered broken? Any other > > > > > > > > > suggestions for a work-around? Would a copy of my configure > > > > > > > > > output help? > > > > > > > > > > > > > > > > > > Malcolm > > > > > > > > > > > > > > > > > > On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote: > > > > > > > > > > the other way to build w/o gui support is to exclude the > > > > > > > > > > tcl and vtk paths in configure. in other works, only vtk > > > > > > > > > > and mni should be included in your configure line. > > > > > > > > > > > > > > > > > > > > On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > > > > > > > > > > > I'm attempting to build the development branch of the > > > > > > > > > > > source code. To reduce dependencies, I'm trying to build > > > > > > > > > > > without any of the GUI support using the flags: > > > > > > > > > > > > > > > > > > > > > > --disable-all-apps > > > > > > > > > > > --disable-gl-apps > > > > > > > > > > > > > > > > > > > > > > It's complaining about a missing dependency: > > > > > > > > > > > > > > > > > > > > > > configure: error: FATAL: libBLT not found. Check > > > > > > > > > > > config.log. Set LDFLAGS or -- with-BLT-dir. > > > > > > > > > > > > > > > > > > > > > > but the instructions imply that BLT is only necessary for > > > > > > > > > > > GUIs. > > > > > > > > > > > > > > > > > > > > > > Are there additional arguments that I need to pass to > > > > > > > > > > > configure? > > > > > > > > > > > > > > > > > > > > > > Malcolm > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the > > > > > > > > > > person to whom it is addressed. If you believe this e-mail > > > > > > > > > > was sent to you in error and the e-mail contains patient > > > > > > > > > > information, please contact the Partners Compliance > > > > > > > > > > HelpLine at http://www.partners.org/complianceline . If > > > > > > > > > > the e-mail was sent to you in error but does not contain > > > > > > > > > > patient information, please contact the sender and > > > > > > > > > > properly dispose of the e-mail. > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
