2. recon-all runs the old fixer 'mris_fix_topology', and if that fails the euler number check, then it runs the new fixer 'mris_topo_fixer'. of course really bad brains fail both.

n. On Mon, 2011-01-17 at 13:56 -0500, Bruce Fischl wrote:

Hi Ilana,

1. This is usually because of big topological defects, in the worst case if

the cerebellum or skull are attached. Look at the end of the recon-all.log and see what it is in the middle of doing. If it's topology fixing, check the inflated.nofix file and see if there is a huge defect.

2. This is also a topology fixer problem. Nick: isn't it only in the new

fixer?

Bruce

On Mon, 17 Jan 2011, Ilana Hairston wrote:

...

Hi there, we are having two unrelated problems with a couple of files:

1. A brain running extremely slow, after initial processing. i.e. we ran

recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted.

thanks ilana

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glad to hear it worked out cheers Bruce On Sat, 22 Jan 2011, Ilana Hairston wrote:

Thanks, We were able to fix the slow processing problem. Since we save separate versions for each topologicl edit step, we can go back if a problem occurs. Indeed when fixing skull strip we edited out some cortex. Without these edits processing ran fine.

So all was not lost, thanks for you help ilana

On 17 January 2011 13:56, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Ilana,

1. This is usually because of big topological defects, in the worst case if

the cerebellum or skull are attached. Look at the end of the recon-all.log and see what it is in the middle of doing. If it's topology fixing, check the inflated.nofix file and see if there is a huge defect.

2. This is also a topology fixer problem. Nick: isn't it only in the new

fixer?

Bruce

On Mon, 17 Jan 2011, Ilana Hairston wrote:

Hi there,

...

we are having two unrelated problems with a couple of files:

1. A brain running extremely slow, after initial processing. i.e. we ran

recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted.

thanks ilana

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