Hi Bruce, I am still confusing about my subjects'recon that I still doubt my skill on detecting the topological error. Therefore, I practice on the FStutorial data and run the mris_euler_number on the "topo_defect_before" to see what happens. The result returns me with 0 holes for all ?h.pial, ?h.white and ?h.inflated.
Can you help me with this problem. Thank, Trinh 2015-10-05 23:09 GMT+07:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Trinh > > the inflated.nofix files are the ones before the topology fixer so they > will always have defects in them > > cheers > Bruce > > On Mon, 5 Oct 2015, Thục Trinh wrote: > > 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. >> >> >> >> > _______________________________________________ > 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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