Good question. You could use different versions for the two steps, but you'd have to report that in your methods, which could get messy. Running pre border.sh with the older caret_command probably wouldn't take that long, but if you tweaked your borders, it could overwrite them, depending on what you used for the borderproj update string (e.g., updated).
To get around that, you could tar/zip just your tweaked borderproj files; re-run preborder.sh; unzip the preserved tweaked borderproj; and run post border.sh. On Nov 27, 2013, at 2:01 PM, Taosheng Liu <[email protected]> wrote: > Thanks for the tip. Just another question, if we switch to the older version, > do you think we should re-run the preborder script as well? or we can pick up > from where preborder has ended and just run postborder with the older > caret_command? > Thank you, > > --ts > > On 11/27/2013 02:33 PM, Donna Dierker wrote: >> 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 <[email protected]> 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 <[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 >>> -- >>> 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
