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



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