By the way I’m also confused on what the effect of increasing/decreasing the mri_segment p threshold will have, I arbitrarily decided to lower the threshold but I’m not sure if that’s what I want On Oct 30, 2013, at 1:22 PM, Jonathan Holt whatsdac@umich.edu wrote:
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
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