Hi Keyma,
I think you're okay. We should probably put a check in the qsphere generation to disable it if the surface is already topologically correct.
cheers, Bruce
On Tue, 3 May 2005, Keyma Prince wrote:
For rh.qsphere and rh.orig I get a total defect index = 0 and 0 holes. Based on what you said, I assume that the topology correction ran ok.
So does this mean it's picking up the fact that I ran the qsphere twice? Can I go ahead with the parcellate_subject despite this?
-Keyma
Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139
On Tue, 3 May 2005, Bruce Fischl wrote:
Hi Keyma,
it means either you didn't run the topology correction, or you run the qsphere generation twice (once before topology correction and once after). Run mris_euler_number on the qsphere and orig surfaces and see what they are.
The qsphere is generated to guide the topology fixing, but is itself not fixed, so it will have the topology of the original ?h.orig surface (that is, it will have a non-zero Euler number usually).
Is that clear? If the orig has a non-zero euler number you'll need to rerun topology correction and everything else that comes after it.
Bruce
On Tue, 3 May 2005, Keyma Prince wrote:
Hi,
When I run check_subject on one of my subject I get the following message:
WARN: rh.qsphere is same size as rh.orig.
I am not sure when the rh.qsphere is generated but can you let me know how to correct this problem so i can continue with parcellate_subject.
thanks, Keyma
Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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