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
