Hi Bruce,
The log file tells that mris_fix_topology did fail (euler number != 2) and that's why the topo_fixer was used.
Ed
On 1 Sep 2009, at 15:12, Bruce Fischl wrote:
did you try using the old (default) topology fixer? Usually mris_fix_topology is called in recon-all unless you specify otherwise.
cheers, Bruce On Tue, 1 Sep 2009, Ed Gronenschild wrote:
Hi,
I got the following error during processing my subject nr 104 with recon-all:
ERROR: - FindPacePath: could not find path.
The error log tells that it occurred during execution of the command
mris_topo_fixer -mgz -warnings 104 rh
What to do?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see. Have you looked at the orig.nofix surface? If there is a huge defect (e.g. cerebellum or skull connected to cortex) then things will fail. Make sure nothing is dramatically wrong with it or the aseg.mgz first.
Bruce
On Tue, 1 Sep 2009, Ed Gronenschild wrote:
Hi Bruce,
The log file tells that mris_fix_topology did fail (euler number != 2) and that's why the topo_fixer was used.
Ed
On 1 Sep 2009, at 15:12, Bruce Fischl wrote:
did you try using the old (default) topology fixer? Usually mris_fix_topology is called in recon-all unless you specify otherwise.
cheers, Bruce On Tue, 1 Sep 2009, Ed Gronenschild wrote:
Hi,
I got the following error during processing my subject nr 104 with recon-all:
ERROR: - FindPacePath: could not find path.
The error log tells that it occurred during execution of the command
mris_topo_fixer -mgz -warnings 104 rh
What to do?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
You're right: the skullstripping didn't go well so that part of the skull is still present. I'll try to fix that. Thanks,
Ed
On 1 Sep 2009, at 16:03, Bruce Fischl wrote:
I see. Have you looked at the orig.nofix surface? If there is a huge defect (e.g. cerebellum or skull connected to cortex) then things will fail. Make sure nothing is dramatically wrong with it or the aseg.mgz first.
Bruce
On Tue, 1 Sep 2009, Ed Gronenschild wrote:
Hi Bruce,
The log file tells that mris_fix_topology did fail (euler number ! = 2) and that's why the topo_fixer was used.
Ed
On 1 Sep 2009, at 15:12, Bruce Fischl wrote:
did you try using the old (default) topology fixer? Usually mris_fix_topology is called in recon-all unless you specify otherwise.
cheers, Bruce On Tue, 1 Sep 2009, Ed Gronenschild wrote:
Hi,
I got the following error during processing my subject nr 104 with recon-all:
ERROR: - FindPacePath: could not find path.
The error log tells that it occurred during execution of the command
mris_topo_fixer -mgz -warnings 104 rh
What to do?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Ed Gronenschild