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 fischl@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 fischl@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.