Hi Anastasia, the files are here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr
The base is here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB Freesurfer outputs: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2 and /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2.long.longbaseTC055FB You should have permissions to see everything, if not, please tell me. Fyi: Maybe it's random, but the 4 errors occurred all in the first time point. Thanks, Vincent > > Hi Vincent - If you upload the tracula dirs for this particular time > point, I'll take a look. > > a.y > > On Mon, 20 May 2013, Vincent Brunsch wrote: > >> Hi Anastasia, >> Thanks for your help! I had this issue with 4 tracts in total. I just >> want to >> add that before rerunning dmri_pathstats not only pathstats.overall but >> also >> pathstats.byvoxel was affected (in the latter there were no matrix >> entries at >> all). >> I found some information in the trac-all.log but not explicitly the >> command >> line <- this was found in pathstats.overall.txt, though. >> >> After rerunning dmri_pathstats everything looks great now for 3 out of >> the 4 >> tracts, YEAH! I am not sure what to do with the last one, though: Here, >> the >> same error occurs but in cpts.map.txt no two lines are identical: >> >> For lh.cst: >> 58 48 10 >> 62 51 21 >> 65 55 26 >> 70 58 35 >> 72 57 39 >> 64 55 56 >> >> Would you suggest deleting randomly one time point for this tract of >> this >> subject? Thanks! >> Vincent >> >> >> Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki: >>> >>> Hi Vincent - Thanks for bringing this to my attention. I can see what >>> might >>> cause this glitch (only in the longitudinal case) and I'll fix it in >>> the >>> next version. >>> >>> In the meantime, if you delete one of the two identical lines from >>> cpts.map.txt, and then rerun the dmri_pathstats command line that >>> you'll >>> find in the trac-all.log of your subject, it should regenerate the >>> stats >>> files correctly. Sorry for the inconvenience. >>> >>> a.y >>> >>> On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote: >>> >>>> Dear Anastasia, >>>> >>>> When running the longitudinal tracula version on our 39 subjects I >>>> found >>>> for some of them "nan"-values for the center_avg variables of some >>>> tracts. >>>> When I have a look at the tract distribution and the highest >>>> probability >>>> path, everything seems to be ok. However, when checking the control >>>> points >>>> of this path, two of them are the same. Do you know how this could >>>> have >>>> happened / what to do? >>>> >>>> E.g. control points of forceps major from a subject (cpts.map.txt), >>>> see >>>> 4th and 5th control point: >>>> >>>> 63 20 39 >>>> 67 31 39 >>>> 59 43 38 >>>> 52 42 38 >>>> 52 42 38 >>>> 43 32 38 >>>> 50 19 33 >>>> >>>> And the respective pathstats.overall.txt: >>>> Count 1500 >>>> Volume 370 >>>> Len_Min 62 >>>> Len_Max 99 >>>> Len_Avg 78.9307 >>>> Len_Center 0 >>>> AD_Avg 0.00155598 >>>> AD_Avg_Weight 0.00158424 >>>> AD_Avg_Center -nan >>>> RD_Avg 0.000438439 >>>> RD_Avg_Weight 0.000401328 >>>> RD_Avg_Center -nan >>>> MD_Avg 0.000810952 >>>> MD_Avg_Weight 0.000795633 >>>> MD_Avg_Center -nan >>>> FA_Avg 0.662419 >>>> FA_Avg_Weight 0.696257 >>>> FA_Avg_Center -nan >>>> >>>> Thanks for your help!! :) >>>> Best, >>>> Vincent >>>> >>>> _______________________________________________ >>>> 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 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.
