It happens when I use -bigventricles.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Chris Adamson
Sent: Thursday, 6 April 2017 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] long mri_ca_register error
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
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