I agree, the check_reg captures look great to me. The 144 cycles are troubling. In your shoes, I'd revert.
On Nov 27, 2013, at 10:41 AM, Taosheng Liu <ts...@msu.edu> wrote: > Hi Donna, > Thanks for testing this, and for your fast response. Yes we're not getting a > core dump and it does finish, although with 144 cycles. Are you saying we > should switch back to the old caret for the time being? I mean, the check_reg > result seems fine, but maybe there's still something wrong with it? > Thank you! > > --ts > > > > On 11/27/2013 11:27 AM, Donna Dierker wrote: >> 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 <do...@brainvis.wustl.edu> 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 <ts...@msu.edu> 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 <ts...@msu.edu> 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 >>>>>> caret-users@brainvis.wustl.edu >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> caret-users@brainvis.wustl.edu >>>>> 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 >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> 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 > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
