Hi Rashmi can you try 5.3 and see if it works? Alternatively you can email me the orig.mgz and I can try it Bruce On Wed, 30 Oct 2013, Rashmi Singh wrote:
> Hey Bruce, > I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check > flags) with a data set that failed showing the same error that I had > received earlier. > I am sure have the correct data set. > I am attaching the recon-all.log and the data. > We have FreeSurfer Version 5.1.0 > Please advice. > Thanks, > Rashmi > > On 10/23/13 9:06 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > >> 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/CombT1T >>> 2Practice/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 >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
