Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T2Practice/FreeSurfer/AA470-2prac/mri
mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux
recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Rashmi
what version are you running? If 5.3, upload the subject and I'll take a look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote:
Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T2Practice/FreeSurfer/AA470-2prac/ mri
mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros)
spacing=8, using 3481 sample points, tol=1.00e-05...
register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux
recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Rashmi Singh