Hi Bruce, I did check the output recon by using mris_euler_number, all the results of ?h.pial, ?.white and also ?h.inflated returned with: 0 holes. But the result from lh.inflated.nofix was: 28 holes. When I load the 3D images of ?h.inflated.nofix in freeview, it appears alot of holes and also handles errors. I wonder about the differences between ?h.inflated and ?h.inflated.nofix. If we want to estimate the quality of recon output, what images we should use?
Thanks and Have a nice day, Trinh 2015-10-02 19:33 GMT+07:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Trinh > > can you just attach the images? Your link didn't work for me. You can > check the topology of the surface computationally using mris_euler_number. > You might also try moving backwards/forwards a few slices to try to > understand what is going on. > > cheers > Bruce > > On Fri, 2 Oct 2015, Thục Trinh wrote: > > >> >> [icon_10_generic_list.png] NCP140539_2_recon.rar >> Hi Freesurfer Experts, >> >> We are on the process of troubleshooting our subjects's recon and we came >> across with this error that we can not determine what kind of problem this >> is: >> It seems there is no white matter and pial errors on all slices as we >> check >> on three different views (sagital,coronal and axial);however, when we load >> rh.inflated.nofix surface on both freeview and tksurfer, there is a big >> difference that at the frontal cortex (area near the medial wall), it >> appears a handle error and also some hole errors on freeview while it does >> not on tksurfer. >> Would you explain how it is visualized that makes us so confused to >> troubleshoot since we can not find anything wrong on white matter volume >> to >> be fixed? >> Here is our data, >> >> Have a nice day, >> >> Trinh >> >> >> > _______________________________________________ > 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. > >
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