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
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