Hi Cindy,
try running it with -no-gcut and see if it helps.
cheers, Bruce
On Mon, 18 Jan 2010, Cindy Eckart wrote:
Dear Freesurfers,
when I try to run the recon-all flow, it exits at the skull stripping stage in some subjects, giving out error messages like this:
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (52, 9, 21) --> (208, 255, 220) using (104, 91, 121) as brain centroid... mean wm in atlas = 126, using box (85,61,96) --> (123, 121,145) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf
When I checked all prior steps, I realized that the nu.mgz was particularly dark and tried to improve it by manually setting control points in the white matter... however, without success, even under inclusion of some control points the skull strip could not be finished....
Then I found a similar problem in the mailing list archive (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007603.htm...), tried the solution proposed there and altered my 001.mgz with a scaling factor of 3 (cp 001.mgz 001_orig.mgz / mri_convert --scale 3 001_orig.mgz 001.mgz / rerun recon-all) again without any success.....
Finally, I have no idea how to find another solution! Has anyone an idea?? Every suggestions is highly appreciated!
Thanks and greetings
Cindy
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