mri_em_register -skull mri/nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9 using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'mri/nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1
total sample mean = 77.6 (1399 zeros)
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spacing=8, using 3243 sample points, tol=1.00e-05...
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register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
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
GCAhistoScaleImageIntensities: could not find wm peak
Numerical result out of range