Hi Cheng
do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look
cheers Bruce
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