Hi,
I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message during skull stripping and the error log reads as follows:
#@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009 /space/raid7/data/london/data/ mri/other/angie/Freesurfer/SUBJECTS_DIR/5003/mri
mri_em_register -skull nu.mgz /space/raid/fmri/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 '/space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca'... 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 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (51, 40, 26) --> (206, 255, 255) using (103, 112, 141) as brain centroid... mean wm in atlas = 126, using box (84,85,113) --> (122, 138,169) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -19541.4 ************************************************ First Search limited to translation only. ************************************************ using real data threshold=42.0
Found translation: (-1.1, 1.1, -17.0): log p = -17915.1 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Linux willis 2.6.27.25-0.1-default #1 SMP 2009-07-01 15:37:09 +0200 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Oct 28 14:45:19 PDT 2009
The error log simply states: CMD mri_watershed
Any advice on how to troubleshoot this problem would be greatly appreciated.
Angie