Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of Iglesias, JE. et al. 2015. Was my computation wrong?
Best, Daniele 2015-11-03 9:37 GMT+01:00 Janosch Linkersdörfer <linkersdoer...@gmail.com>: > Hi Anastasia and list, > > sorry, I just now got around to testing out the new build of dmri_paths > you sent me. Sadly, the results look about the same: > > > > > Here the path stats file for the left SLFt: > > > > What could be the problem?! I think I did what you suggested: > > - install the new version of dmri_paths ( > https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it > executable > - rerun trac-all -path for the subjects with only one time point > - rerun trac-all -stat for all subjects > > Also: Is that problem only a visualization problem, or does it also mean > that the values I get for a participant at a specific part of a tract are > not aligned and I cannot analyze the data in that way? > > Thanks for your help!! > > Best, > > Janosch > > > > On 20 Aug 2015, at 21:35, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > > > > > > Hi Janosch - Indeed, someone has to be first. I'll send you a fresh > build of dmri_paths tomorrow. You'll have to replace your copy of > $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" > only for the subjects that have 1 time point. Then rerun "trac-all -stat" > with all subjects together. And then tell us what other problem you find :) > > > > Best, > > a.y > > > > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: > > > >> Hey Anastasia, > >> > >>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu>: > >>> > >>> > >>> Hi Janosch - There is a bug in how the output paths are saved when > longitudinal TRACULA is run with one time point only. I'm working on a fix. > >> > >> OK, then I'm relieved that it isn't an error on my side. Thank you very > much for looking into it! > >> > >>> In the meantime, you can try your analysis with the subjects that have > multiple time points and you won't be affected by this problem. I can see > that the subjects with a single time point are about 1/3 of your sample, > and so you may not want to drop them completely. > >> > >> Yeah, it's children's data, so I'm happy about every measurement we > got. I'll be waiting for the fixed script to be able to include all > subjects in the analysis... > >> > >>> > >>> Thank you for trying things that nobody else has tried and finding > these bugs! > >> > >> Somebody has to be the first, eh? :) > >> > >> Thank you very much, > >> > >> Janosch > >> > >>> > >>> More soon, > >>> a.y > >>> > >>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: > >>> > >>>> Hey Anastasia, > >>>> > >>>> thanks for looking into this. > >>>> > >>>>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu>: > >>>>> > >>>>> > >>>>> Hi Janosch - Looking at the stats files of your subjects, just by a > quick count of the number of lines, I see that there are some subjects that > have only 1 time point and some that have multiple time points, and that > the pathstats.byvoxel.txt files have different lengths between those two > types of subjects. > >>>>> > >>>>> I suspect that the strange average path that you get has to do with > how this mixing of subjects was done. Did you run the subjects with a > single time point through the longitudinal stream as well? > >>>> > >>>> Yes, I ran the longitudinal stream for all subjects, also for the > ones with only one time point. > >>>> > >>>> Thanks, > >>>> > >>>> Janosch > >>>> > >>>>> > >>>>> Best, > >>>>> a.y > >>>>> > >>>>> On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: > >>>>> > >>>>>> Hi Anastasia, > >>>>>> > >>>>>> yes, I am. But it looks similar in the distributed version :( > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Janosch > >>>>>> > >>>>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu>: > >>>>>>> > >>>>>>> > >>>>>>> Hi Janosch - Are you by any chance using the dev version of > freeview? > >>>>>>> > >>>>>>> a.y > >>>>>>> > >>>>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: > >>>>>>> > >>>>>>>> Hi Anastasia and list, > >>>>>>>> > >>>>>>>> I'm trying to do analyses along the tract with the > path_stats_byvoxel files. > >>>>>>>> > >>>>>>>> When I am visualizing the points using the waypoint functionality > of Freeview, it looks a little strange, i.e., the points are not equally > spaces on the tract, but clumped together at some parts and spread out on > others, see: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> this looks different to your slides: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Also, the most posterior points seem to be strangely located (in > the other hemisphere). What could be the reason for this strange behavior? > >>>>>>>> > >>>>>>>> Thanks, > >>>>>>>> > >>>>>>>> Janosch > >>>>>>> > >>>>>>> > >>>>>>> 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. > >>>>>> > >>>>>> > >>>>>> > >>>> > >>>> > >>>> > >> > >> > >> > > > _______________________________________________ > 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. > > -- _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorla...@fatebenefratelli.it; daniele.orlandi....@gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)
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