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Hi experts,
While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag.
The error message is the following:
register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range
I tried the following suggestion in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but to no avail.
It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff.
Any suggestions would be helpful. Best, Julia Shin