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