Hi guys,

I am having a bit of trouble with expert options... 

I ran:

recon-all -autorecon2 -autorecon3 -expert expert.opts -s <SUBJID>

my expert options file reads:

mri_segment -p 0.70 

and recon-all exits with errors right after this output:

using 70% threshold

mri_read(): couldn't determine type of file /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/s_100930ct/mri/0.70

mri_segment: could not read source volume from 0.70

What have I done incorrectly?

On Tue, Oct 29, 2013 at 2:25 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile

On Mon, 28 Oct 2013, Jon Holt wrote:

Where can I find more info on expert opts?

On Oct 28, 2013, at 6:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Jon
The segmentation looks really poor, which probably causes a topological defect resulting in what you see. I would try using expert opts to set the segmentation thresholds better
Cheers
Bruce

On Oct 28, 2013, at 1:10 PM, Jonathan Holt <whatsdac@umich.edu> wrote:

FS experts,

both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed?

Jon

<Screen Shot 2013-10-21 at 2.07.12 PM.png><Screen Shot 2013-10-21 at 2.06.20 PM.png>
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