Hi there,
I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this?
Many thanks ,
Julia Hill Research Assistant School of Psychiatry University of New South Wales
Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
Hi Julia Does the stuff left around mess anything up? You are probably fine running it that way Bruce
On Nov 8, 2011, at 9:30 PM, Julia Hill julia.hill@neura.edu.au wrote:
Hi there,
I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this?
Many thanks,
Julia Hill Research Assistant School of Psychiatry University of New South Wales
Previously Prince of Wales Medical Research Institute
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
<badskullstrip1.tiff> <badskullstrip2.tiff> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can try running just recon-all -skullstrip first, if that doesn't fix the problem, you can try changing the wsthresh and removing the -no-wsgcaatlas flag (or add the flag if you didn't include it). Sometimes that makes a difference.
-Khoa
On Wed, 9 Nov 2011, Julia Hill wrote:
Hi there,
I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this?
Many thanks ,
Julia Hill Research Assistant School of Psychiatry University of New South Wales
Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Julia Hill -
Khoa Nguyen