On Wed, 23
Jul 2014, Cheng Peng wrote:

> 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