Hi Taosheng, I tried running postborder.sh on a dataset I have here, and I got a core dump on the offending line:
+ caret_command -surface-sphere-multi-morph Human.SAIS_018.L.73730.spec deformed_Human.SAIS_018.L.Midthickness_711-2B.mws.coord Human.SAIS_018.L.SPHERICAL.73730.MWS.coord Human.SAIS_018.L.CLOSED.73730.topo ./PALS_B12.LR/postborder.sh: line 50: 27257 Segmentation fault (core dumped) caret_command -surface-sphere-multi-morph $SPEC $FIDUCIAL_MWS $SPHERE_MWS $TOPO You're not getting a core dump, but something else is clearly going awry with that line. I tried backtracking to a June 2011 vintage caret, and it completed with no problems. Here is the version I used: http://brainvis.wustl.edu/pub/caret/caret_distribution_Linux64.v5.64.zip login pub password download Here are the logs for the for the two versions of caret (bad and good): Problem log: http://brainmap.wustl.edu/pub/donna/US/MI/postborder.log Good log: http://brainvis.wustl.edu/pub/donna/US/MI/postborder.201106.log I'm not sure when caret_command will be fixed, but I will pass the dataset and details on to the developers. Donna On Nov 26, 2013, at 11:58 AM, Donna Dierker <[email protected]> wrote: > Hi Taosheng, > > I am going to try postborder.sh on my new Linux box and see if it does the > same thing. > > I don't see any candidate culprits in my ~/.caret5_preferences file. > > No one else has reported this issue. More users are moving to the fs_LR > pipeline: > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR > > There are trade-offs which are discussed here: > > http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html > > One big plus is that there is no border tweaking. > > I'll let you know how my post border.sh trial comes out, or if I need sample > data. But I think I have plenty of sample data right here. I can't imagine > what might be unique about our data that would cause this. > > Donna > > > On Nov 26, 2013, at 8:22 AM, Taosheng Liu <[email protected]> wrote: > >> Hi Donna, >> Yes I can see that line of code in the script. Have you other others on this >> list run this command lately? I wonder if you also see this many cycles. If >> not, I wonder if there is some global setting I should set, or something is >> off with my data. I can certainly supply the data if needed. >> Thank you, >> >> --Taosheng >> >> >> On 11/25/2013 06:50 PM, Donna Dierker wrote: >>> Hmmm. Your results look great, but 144 cycles of spherical morphing is >>> certainly not normal. I think the line in the script that does this is >>> this one: >>> >>> #MULTIRESOLUTION MORPHING >>> caret_command -surface-sphere-multi-morph $SPEC $FIDUCIAL_MWS >>> $SPHERE_MWS $TOPO >>> >>> There are no parameters for this one; they are built in, apparently, so I'm >>> not sure what could be going on. >>> >>> I'm stumped. >>> >>> >>> On Nov 25, 2013, at 4:27 PM, Taosheng Liu <[email protected]> wrote: >>> >>>> Hi Donna, >>>> I've been using the preborder and postborder scripts to convert files from >>>> FreeSurfer to Caret (hope you still remember I was involved in early >>>> testing of these scripts). Things have been working great. I haven't done >>>> this for a while, but recently I changed computer and installed the >>>> current version of Caret and these scripts, and there seems to be some >>>> difference in how the code works. I just want to make sure this is >>>> expected behavior. >>>> Specifically, when we run postborder script, it takes much longer. It >>>> seems either the script or caret_command is doing more iterations, because >>>> we now see files like this after the script finishes: >>>> >>>> Human.FS040.L.SPHERICAL.73730.MWS.SPHERE_CYCLE144.coord >>>> >>>> There're a lot of files like this, with consecutive names from CYCLE1 to >>>> CYCLE 144, whereas previously it only goes from CYCLE1 to CYCLE4. My >>>> question is: is this expected behavior, or is there something wrong in how >>>> we ran the scripts? >>>> I've posted the result from the check_reg here >>>> http://psychology.msu.edu/liulab/files/html_out/views.html >>>> >>>> They look just like before, but I'd like to confirm whether this is normal. >>>> Thank you very much, >>>> >>>> --Taosheng >>>> >>>> -- >>>> Taosheng Liu >>>> Assistant Professor >>>> Department of Psychology >>>> Michigan State University >>>> 316 Physics Road >>>> East Lansing, MI 48824 >>>> PH: 517.432.6694 >>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> -- >> Taosheng Liu >> Assistant Professor >> Department of Psychology >> Michigan State University >> 316 Physics Road >> East Lansing, MI 48824 >> PH: 517.432.6694 >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
