Hi, Freesurfer experts:
I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary)
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