egister_mri: find_optimal_transform
find_optimal_transform: nsamples 2185, passno 0, spacing 8
GCAhistoScaleImageIntensities: could not find wm peak
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=0.0
skull bounding box = (0, 0, 0) --> (255, 255, 255)
using (85, 85, 128) as brain centroid...
mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI wm
WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1
before smoothing, mri peak at 0
WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1,
mri_peak=-1
after smoothing, mri peak at 0, scaling input intensities by inf
It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error
message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image.
Thanks!
Best Regards,
Cheng Peng
Maryland Neuroimaging Center