Dear freesurfer specialists,
we just ran a sample of 91 subjects (with 3 timepoints), and in 5 of them the following problem occured: freesurfer exited with error in autorecon1 during skull stripping. The protocol looks like this:
#-------------------------------------------- #@# Skull Stripping Thu Sep 17 18:13:23 CEST 2009 /Applications/freesurfer/subjects/1115is05B/mri \n mri_em_register -skull nu.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta \n aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/Applications/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 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=9.0 skull bounding box = (51, 10, 25) --> (205, 255, 237) using (102, 92, 131) as brain centroid... mean wm in atlas = 126, using box (83,62,105) --> (120, 122,157) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-bxp-164-3.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386
recon-all exited with ERRORS at Thu Sep 17 18:14:19 CEST 2009
We are pretty much freesurfer beginners and don't have a clue what kind of mistake this could be. We couldn't find any obvious differnces to our other subjects which ran fine. I also attach the whole recon-all.log file, just in case a problem occured on a previous stage we didn't recognize. We used a MacPro3,1 and Freesurfer version 4.2.0.
Thank you for your help!
Best, Elisabeth and Genia
Hi Elisabeth,
try running recon-all with -no-wsgcaatlas and see if that fixes your problem.
cheers, Bruce
On Mon, 19 Apr 2010, Wenger, Elisabeth wrote:
Dear freesurfer specialists,
we just ran a sample of 91 subjects (with 3 timepoints), and in 5 of them the following problem occured: freesurfer exited with error in autorecon1 during skull stripping. The protocol looks like this:
#-------------------------------------------- #@# Skull Stripping Thu Sep 17 18:13:23 CEST 2009 /Applications/freesurfer/subjects/1115is05B/mri \n mri_em_register -skull nu.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta \n aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/Applications/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 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=9.0 skull bounding box = (51, 10, 25) --> (205, 255, 237) using (102, 92, 131) as brain centroid... mean wm in atlas = 126, using box (83,62,105) --> (120, 122,157) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-bxp-164-3.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386
recon-all exited with ERRORS at Thu Sep 17 18:14:19 CEST 2009
We are pretty much freesurfer beginners and don't have a clue what kind of mistake this could be. We couldn't find any obvious differnces to our other subjects which ran fine. I also attach the whole recon-all.log file, just in case a problem occured on a previous stage we didn't recognize. We used a MacPro3,1 and Freesurfer version 4.2.0.
Thank you for your help!
Best, Elisabeth and Genia
Dear Freesurfer specialists,
to fix the skull stripping error, i tried running "recon-all with -no-wsgcaatlas", as you suggested. This seems to have fixed the skull stripping thing, but now there is again an error in the EM registration step - just as in a few other subjects of our sample... The script looks like this:
#@# EM Registration Thu Apr 22 11:24:12 CEST 2010 /Applications/freesurfer/subjects/1115is05B/mri \n mri_em_register -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_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=12.0 skull bounding box = (61, 33, 24) --> (195, 145, 204) using (106, 70, 114) as brain centroid... mean wm in atlas = 107, using box (90,56,92) --> (122, 83,136) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-OSX-164-15.local 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Thu Apr 22 11:26:00 CEST 2010
Again, i attach the full recon-log file. Thanks a lot a lot a lot for your help!!
Best, Elisabeth
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Wenger, Elisabeth