Freesurfer devs,
In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem?
Cheers,
Chris.
mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat -bigventricles -smoothness 0.5 -levels 2 -A 1 -l *base*/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
handling expanded ventricles... l_smoothness = 0.50 levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) TransformSample: gcam has not been inverted! freeing gibbs priors...done. average std[0] = 5.0 setting orig areas to linear transform determinant scaled 8.40 writing talairach.invalid.mgz writing talairach.status.mgz registering ventricular system... using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 5.0) distributions for initial ventricular estimate No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory TransformSample: gcam has not been inverted! No such file or directory
Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au www.mcri.edu.auhttp://www.mcri.edu.au/
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