When I am trying to use verbena, it runs for awhile and then provides no output and an error message. I cannot find were it saves the logfile, if any, so I don't know how to further trouble shoot. I think the "STL exception" is causing the problem, though "Cannot open volume ... for reading" makes me wonder.
When the command finishes:
~/nifti_files/twistns/DSC/vm is empty, and the /tmp/fsl_QIn4PB_verbena/vm/ directory doesn't exist.
Any help would be very much appreciated.
Thank you,
Jeff
verbena -i 4D_FSL_TWIST.nii.gz -a 4D_FSL_TWIST_AIF.nii.gz -o ~/nifti_files/twistns/DSC -m 4D_FSL_TWIST_mask_sm.nii.gz -tr 0.78 -te 0.0011
Begin VM analysis
rm: cannot remove 'vm*': No such file or directory
------------------
Welcome to FABBER v2.0
Logfile started: vm/logfile
Start time: Thu Jul 18 11:17:17 2019
FABBER release v2.0
Forward Model version:
$Id: fwdmodel_dsc.cc,v 1.14 2015/09/08 14:07:51 mwebster Exp $
Expanded, --param-spatial-priors=NNNNM
Loading mask data from 'mask'
Loading supplementary data from 'aif'
Loading data from 'data'
WARNING ONCE: Not saving finalSpatialPriors.nii.gz -- too huge!!
Using initial value for all deltas: 0.5
Starting iteration 1 of 20
(it runs for 19 iterations, then:)
Starting iteration 20 of 20
k=1, tmp1=1.5e+15, tmp2=1.82416e-17
k=2, tmp1=875.4, tmp2=0
k=3, tmp1=8754, tmp2=0
k=4, tmp1=218850, tmp2=0
k=5, tmp1=124043, tmp2=37176.7
New akmean: 1.4953e-12 2.5617e+00 2.5622e-01 1.0249e-02 1.3913e-02
Optimizing for parameter 1
SpatialPrior 1 type N : 0 0 0
delta(k) = 0, rho(k) == 0
Optimizing for parameter 2
SpatialPrior 2 type N : 0 0 0
delta(k) = 0, rho(k) == 0
Optimizing for parameter 3
SpatialPrior 3 type N : 0 0 0
delta(k) = 0, rho(k) == 0
Optimizing for parameter 4
SpatialPrior 4 type N : 0 0 0
delta(k) = 0, rho(k) == 0
Optimizing for parameter 5
SpatialPrior 5 type M : 0.0139127 0 0
delta(k) = -3, rho(k) == 1234.57
Coefficient resels per voxel for param 1: 0.923695 (vb) or -999 (eo)
Coefficient resels per voxel for param 2: 0 (vb) or -999 (eo)
Coefficient resels per voxel for param 3: 0 (vb) or -999 (eo)
Coefficient resels per voxel for param 4: 0 (vb) or -999 (eo)
Coefficient resels per voxel for param 5: 0.0704702 (vb) or -999 (eo)
error: subview::diag(): requested diagonal out of bounds
Summary of warnings (2 distinct warnings)
Issued 80 times: Cache is disabled to avoid memory problems!
Issued once: Not saving finalSpatialPriors.nii.gz -- too huge!!
STL exception caught in fabber:
subview::diag(): requested diagonal out of bounds
Logfile was: vm/logfile
Cannot open volume /tmp/fsl_QIn4PB_verbena/vm/mean_transitm for reading!
Cannot open volume /tmp/fsl_QIn4PB_verbena/vm/mean_lambda for reading!
Tidying up
Verbena done
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