Dear Lilla and freesurfers,
I hvae tried to rub the mri_CVS_register and got the following error:
VolumeMorph load - failed to open input stream.
I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Any idea how to fix this>
Log file atttached
Thanks!
Shani
On Fri, Oct 30, 2015 at 11:17 PM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu>
wrote:
>
> Hi Shani,
>
> Sure. You can do
>
> mri_cvs_register --help
>
> and that should give you lots of information.
>
> Alternatively you can also go to
> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register
>
> and read through the presentation that we give at the FS course:
> http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt
>
> Best, Lilla
>
>
> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>
>
>> Hello
>> Can you please direct me to more information about the CVS.
>> Thanks!
>> Shani
>>
>> בתאריך 30 באוק' 2015 14:39, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
>> כתב:
>> Hi Shani
>>
>> you can use mri_vol2vol with the talairach.m3z. Alternatively, you
>> can run CVS which will give you more accurate cortical matching and use the
>> transform that it produces.
>>
>> cheers
>> Bruce
>> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>>
>> Dear freesurfers,
>> I would like to know what will be the best way to bring
>> volumes in the
>> individual subject's space to the fsaverage space.
>>
>> Thanks,
>> Shani
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
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> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
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>
>
Logfile for mri_cvs_register
Sun Nov 1 22:32:09 EET 2015
--mov RETU
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
yaniva17
Linux yaniva17 3.2.0-90-generic #128-Ubuntu SMP Fri Aug 14 21:43:58 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
asegfname aseg
Using m3z type morph files.
mri_cvs_register: Step 1 (spherical registration) took 0 seconds
surf2vol -fixed_mri /usr/local/freesurfer/subjects//cvs_avg35/mri//norm.mgz -moving_mri /media/drivee/subjects/RETU/mri//norm.mgz -fixed_surf /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.white -moving_surf /media/drivee/subjects/RETU/cvs/lh.resample.white -fixed_surf_2 /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.white -moving_surf_2 /media/drivee/subjects/RETU/cvs/rh.resample.white -fixed_surf_3 /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.pial -moving_surf_3 /media/drivee/subjects/RETU/cvs/lh.resample.pial -fixed_surf_4 /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.pial -moving_surf_4 /media/drivee/subjects/RETU/cvs/rh.resample.pial -aparc /usr/local/freesurfer/subjects//cvs_avg35/label//lh.aparc.annot -aparc_2 /usr/local/freesurfer/subjects//cvs_avg35/label//rh.aparc.annot -aparc_3 /usr/local/freesurfer/subjects//cvs_avg35/label//lh.aparc.annot -aparc_4 /usr/local/freesurfer/subjects//cvs_avg35/label//rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -topology_old -compress -pc_type jacobi -ksp_type preonly -ksp_view -ksp_converged_reason -poisson .3 -young 1000 -cache_transform /media/drivee/subjects/RETU/cvs/transform.txt -out /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35.mgz -out_mesh /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35 -out_affine /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35.affine.mgz
No ASEG option present
No field output option specified
will use default value out_field.mgz
will cache transform in file /media/drivee/subjects/RETU/cvs/transform.txt
reading fixed volume
reading moving volume
surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.white type = 0
surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.white type = 0
surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.pial type = 1
surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.pial type = 1
processing APARC
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
label = unknown -> value = 0
label = corpuscallosum -> value = 4
ignored labels = 0 4
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
label = unknown -> value = 0
label = corpuscallosum -> value = 4
ignored labels = 0 4
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
label = unknown -> value = 0
label = corpuscallosum -> value = 4
ignored labels = 0 4
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
label = unknown -> value = 0
label = corpuscallosum -> value = 4
ignored labels = 0 4
surface name = /media/drivee/subjects/RETU/cvs/lh.resample.white type = 0
surface name = /media/drivee/subjects/RETU/cvs/rh.resample.white type = 0
surface name = /media/drivee/subjects/RETU/cvs/lh.resample.pial type = 1
surface name = /media/drivee/subjects/RETU/cvs/rh.resample.pial type = 1
trying to read transform from /media/drivee/subjects/RETU/cvs/transform.txt
done with Powell
applying linear transform to MOVING surf pos.
linear transform =
1.04128 -0.0738084 -0.0714516
0.0511188 1.07897 0.133787
0.066052 -0.100597 1.0632
-16.4102 1.6557 -10.649
linear transform =
1.04128 -0.0738084 -0.0714516
0.0511188 1.07897 0.133787
0.066052 -0.100597 1.0632
-16.4102 1.6557 -10.649
linear transform =
1.04128 -0.0738084 -0.0714516
0.0511188 1.07897 0.133787
0.066052 -0.100597 1.0632
-16.4102 1.6557 -10.649
linear transform =
1.04128 -0.0738084 -0.0714516
0.0511188 1.07897 0.133787
0.066052 -0.100597 1.0632
-16.4102 1.6557 -10.649
DONE
direct min = 62.3002 45.1985 37.6148 direct max = 195.891 164.948 215.515
bounding box elts =
min = 52.3002 35.1985 27.6148
max = 205.891 174.948 225.515
DIRTY value = 1
create BC container - ripCounter = 0
create BC container - ripCounter = 0
create BC container - ripCounter = 0
create BC container - ripCounter = 0
creating container for the mesher
writing surface to file lh.dbg_surf.white
writing surface to file rh.dbg_surf.white
writing surface to file lh.dbg_surf.pial
writing surface to file rh.dbg_surf.pial
srcPoints size = 0
======================
step = 17
===============
elt_vol= 10
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 20.19
Smoothing mesh.
Smooth seconds: 1.12
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.09
Total running seconds: 21.4
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 121828
Mesh tetrahedra: 739056
Mesh faces: 1494319
Mesh subfaces: 32414
Mesh subsegments: 626
mesh nodes = 121828 mesh elts = 739056
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
InitializeOctantDeterminant
count inserted = 100000 elapsed = 0.154 seconds element count = 800208
count inserted = 200000 elapsed = 0.279 seconds element count = 2422080
count inserted = 300000 elapsed = 0.242 seconds element count = 4013438
count inserted = 400000 elapsed = 0.2 seconds element count = 5467196
count inserted = 500000 elapsed = 0.184 seconds element count = 6883637
count inserted = 600000 elapsed = 0.172 seconds element count = 8299698
count inserted = 700000 elapsed = 0.167 seconds element count = 9718960
done building octree - total elements = 10276256
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 143223
Total BCs = 548640
no-eqs = 365484
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=365484, cols=365484
total: nonzeros=16883430, allocated nonzeros=16883727
using I-node routines: found 121844 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=365484, cols=365484
total: nonzeros=16883430, allocated nonzeros=16883727
using I-node routines: found 121844 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 114374
countInvalid = 4 general-count = 548636
Average of the error norm = 0.13123
Initial error = 0.433653
Average of the error norm conditional = 0.131467
Active Residual error = 0.0343243
Total error = 0.131234
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 156452
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 489
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 179021
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 525
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 7.01982
Max after displacement = 35.6159
Error points = 0
======================
step = 16
===============
elt_vol= 9.6875
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 21.15
Smoothing mesh.
Smooth seconds: 1.17
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.09
Total running seconds: 22.41
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 125414
Mesh tetrahedra: 761432
Mesh faces: 1539405
Mesh subfaces: 33082
Mesh subsegments: 630
mesh nodes = 125414 mesh elts = 761432
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.147 seconds element count = 777689
count inserted = 200000 elapsed = 0.262 seconds element count = 2363228
count inserted = 300000 elapsed = 0.247 seconds element count = 3933296
count inserted = 400000 elapsed = 0.202 seconds element count = 5365337
count inserted = 500000 elapsed = 0.187 seconds element count = 6763367
count inserted = 600000 elapsed = 0.178 seconds element count = 8155457
count inserted = 700000 elapsed = 0.166 seconds element count = 9542076
done building octree - total elements = 10408660
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 143443
Total BCs = 548640
no-eqs = 376242
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=376242, cols=376242
total: nonzeros=17389050, allocated nonzeros=17389338
using I-node routines: found 125430 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=376242, cols=376242
total: nonzeros=17389050, allocated nonzeros=17389338
using I-node routines: found 125430 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 117313
countInvalid = 2 general-count = 548638
Average of the error norm = 0.137181
Initial error = 0.43873
Average of the error norm conditional = 0.137317
Active Residual error = 0.035905
Total error = 0.137183
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 186778
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 516
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 6.672
Max after displacement = 33.9369
Error points = 0
======================
step = 15
===============
elt_vol= 9.375
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0.01
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 22.43
Smoothing mesh.
Smooth seconds: 1.24
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.1
Total running seconds: 23.79
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 129545
Mesh tetrahedra: 786982
Mesh faces: 1590880
Mesh subfaces: 33832
Mesh subsegments: 637
mesh nodes = 129545 mesh elts = 786982
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.151 seconds element count = 761066
count inserted = 200000 elapsed = 0.269 seconds element count = 2310044
count inserted = 300000 elapsed = 0.254 seconds element count = 3851314
count inserted = 400000 elapsed = 0.211 seconds element count = 5261740
count inserted = 500000 elapsed = 0.199 seconds element count = 6633990
count inserted = 600000 elapsed = 0.182 seconds element count = 7994271
count inserted = 700000 elapsed = 0.178 seconds element count = 9357578
done building octree - total elements = 10553552
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 143508
Total BCs = 548640
no-eqs = 388635
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=388635, cols=388635
total: nonzeros=17967237, allocated nonzeros=17967525
using I-node routines: found 129561 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=388635, cols=388635
total: nonzeros=17967237, allocated nonzeros=17967525
using I-node routines: found 129561 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 118844
countInvalid = 0 general-count = 548640
Average of the error norm = 0.143487
Initial error = 0.444793
Average of the error norm conditional = 0.143771
Active Residual error = 0.0376083
Total error = 0.143487
c0324 time elapsed updating the sources (seconds) = 0
NO ORIENTATION PBs FOUND !!!
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 6.32654
Max after displacement = 32.5255
Error points = 0
======================
step = 14
===============
elt_vol= 9.0625
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.01
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 23.53
Smoothing mesh.
Smooth seconds: 1.29
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.1
Total running seconds: 24.95
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 133841
Mesh tetrahedra: 814143
Mesh faces: 1645510
Mesh subfaces: 34448
Mesh subsegments: 647
mesh nodes = 133841 mesh elts = 814143
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.161 seconds element count = 744132
count inserted = 200000 elapsed = 0.271 seconds element count = 2254138
count inserted = 300000 elapsed = 0.254 seconds element count = 3763729
count inserted = 400000 elapsed = 0.211 seconds element count = 5152505
count inserted = 500000 elapsed = 0.201 seconds element count = 6505094
count inserted = 600000 elapsed = 0.182 seconds element count = 7838809
count inserted = 700000 elapsed = 0.176 seconds element count = 9172072
count inserted = 800000 elapsed = 0.168 seconds element count = 10521287
done building octree - total elements = 10713157
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 143999
Total BCs = 548640
no-eqs = 401523
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=401523, cols=401523
total: nonzeros=18577689, allocated nonzeros=18577968
using I-node routines: found 133857 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=401523, cols=401523
total: nonzeros=18577689, allocated nonzeros=18577968
using I-node routines: found 133857 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 122971
countInvalid = 0 general-count = 548640
Average of the error norm = 0.151355
Initial error = 0.451889
Average of the error norm conditional = 0.151202
Active Residual error = 0.0396875
Total error = 0.151355
c0324 time elapsed updating the sources (seconds) = 0
NO ORIENTATION PBs FOUND !!!
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 5.98508
Max after displacement = 30.6955
Error points = 0
======================
step = 13
===============
elt_vol= 8.75
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.02
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 23.58
Smoothing mesh.
Smooth seconds: 1.33
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.11
Total running seconds: 25.05
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 138646
Mesh tetrahedra: 843658
Mesh faces: 1704935
Mesh subfaces: 35238
Mesh subsegments: 650
mesh nodes = 138646 mesh elts = 843658
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.157 seconds element count = 719901
count inserted = 200000 elapsed = 0.272 seconds element count = 2196924
count inserted = 300000 elapsed = 0.253 seconds element count = 3672665
count inserted = 400000 elapsed = 0.213 seconds element count = 5039310
count inserted = 500000 elapsed = 0.2 seconds element count = 6364054
count inserted = 600000 elapsed = 0.177 seconds element count = 7664797
count inserted = 700000 elapsed = 0.177 seconds element count = 8974253
count inserted = 800000 elapsed = 0.165 seconds element count = 10289908
done building octree - total elements = 10868562
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 144402
Total BCs = 548640
no-eqs = 415938
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=415938, cols=415938
total: nonzeros=19245768, allocated nonzeros=19246065
using I-node routines: found 138662 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=415938, cols=415938
total: nonzeros=19245768, allocated nonzeros=19246065
using I-node routines: found 138662 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 128622
countInvalid = 0 general-count = 548640
Average of the error norm = 0.161598
Initial error = 0.460384
Average of the error norm conditional = 0.160841
Active Residual error = 0.0423357
Total error = 0.161598
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 162537
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 489
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 5.64796
Max after displacement = 28.7837
Error points = 0
======================
step = 12
===============
elt_vol= 8.4375
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.02
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 26.25
Smoothing mesh.
Smooth seconds: 1.47
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.11
Total running seconds: 27.87
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 143578
Mesh tetrahedra: 874299
Mesh faces: 1766701
Mesh subfaces: 36206
Mesh subsegments: 656
mesh nodes = 143578 mesh elts = 874299
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.164 seconds element count = 705319
count inserted = 200000 elapsed = 0.278 seconds element count = 2138835
count inserted = 300000 elapsed = 0.261 seconds element count = 3589369
count inserted = 400000 elapsed = 0.225 seconds element count = 4932323
count inserted = 500000 elapsed = 0.202 seconds element count = 6233011
count inserted = 600000 elapsed = 0.187 seconds element count = 7508878
count inserted = 700000 elapsed = 0.18 seconds element count = 8791377
count inserted = 800000 elapsed = 0.171 seconds element count = 10082029
done building octree - total elements = 11044422
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 145412
Total BCs = 548640
no-eqs = 430734
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=430734, cols=430734
total: nonzeros=19939182, allocated nonzeros=19939479
using I-node routines: found 143594 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=430734, cols=430734
total: nonzeros=19939182, allocated nonzeros=19939479
using I-node routines: found 143594 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 136504
countInvalid = 2 general-count = 548638
Average of the error norm = 0.172908
Initial error = 0.470651
Average of the error norm conditional = 0.17138
Active Residual error = 0.0454314
Total error = 0.172916
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 314478
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 930
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 5.31431
Max after displacement = 27.178
Error points = 0
======================
step = 11
===============
elt_vol= 8.125
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.03
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 24.61
Smoothing mesh.
Smooth seconds: 1.38
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.11
Total running seconds: 26.14
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 149030
Mesh tetrahedra: 908643
Mesh faces: 1835848
Mesh subfaces: 37124
Mesh subsegments: 663
mesh nodes = 149030 mesh elts = 908643
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.159 seconds element count = 684773
count inserted = 200000 elapsed = 0.259 seconds element count = 2080118
count inserted = 300000 elapsed = 0.245 seconds element count = 3502535
count inserted = 400000 elapsed = 0.207 seconds element count = 4823279
count inserted = 500000 elapsed = 0.19 seconds element count = 6093981
count inserted = 600000 elapsed = 0.173 seconds element count = 7344434
count inserted = 700000 elapsed = 0.16 seconds element count = 8600330
count inserted = 800000 elapsed = 0.161 seconds element count = 9852476
count inserted = 900000 elapsed = 0.147 seconds element count = 11119394
done building octree - total elements = 11229546
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 146082
Total BCs = 548640
no-eqs = 447090
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=447090, cols=447090
total: nonzeros=20712858, allocated nonzeros=20713146
using I-node routines: found 149046 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=447090, cols=447090
total: nonzeros=20712858, allocated nonzeros=20713146
using I-node routines: found 149046 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 143591
countInvalid = 4 general-count = 548636
Average of the error norm = 0.18591
Initial error = 0.483101
Average of the error norm conditional = 0.183479
Active Residual error = 0.0488649
Total error = 0.185931
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 165294
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 501
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 135537
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 462
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_11
Initial transform
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 4.98358
Max after displacement = 26.1294
Error points = 0
======================
step = 10
===============
elt_vol= 7.8125
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.04
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 25.65
Smoothing mesh.
Smooth seconds: 1.46
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.11
Total running seconds: 27.27
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 154826
Mesh tetrahedra: 944379
Mesh faces: 1907819
Mesh subfaces: 38122
Mesh subsegments: 667
mesh nodes = 154826 mesh elts = 944379
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.157 seconds element count = 664880
count inserted = 200000 elapsed = 0.26 seconds element count = 2012211
count inserted = 300000 elapsed = 0.26 seconds element count = 3410334
count inserted = 400000 elapsed = 0.217 seconds element count = 4711853
count inserted = 500000 elapsed = 0.187 seconds element count = 5949651
count inserted = 600000 elapsed = 0.177 seconds element count = 7178811
count inserted = 700000 elapsed = 0.169 seconds element count = 8409641
count inserted = 800000 elapsed = 0.16 seconds element count = 9633048
count inserted = 900000 elapsed = 0.152 seconds element count = 10866951
done building octree - total elements = 11419070
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 147040
Total BCs = 548640
no-eqs = 464478
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=464478, cols=464478
total: nonzeros=21521562, allocated nonzeros=21521859
using I-node routines: found 154842 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=464478, cols=464478
total: nonzeros=21521562, allocated nonzeros=21521859
using I-node routines: found 154842 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 150768
countInvalid = 1 general-count = 548639
Average of the error norm = 0.201277
Initial error = 0.498349
Average of the error norm conditional = 0.196638
Active Residual error = 0.0527052
Total error = 0.201279
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 186524
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 495
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 171244
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 507
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_10
Initial transform
name = compressed_step_11
Initial transform
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 4.65335
Max after displacement = 24.5705
Error points = 0
======================
step = 9
===============
elt_vol= 7.5
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.04
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 27.5
Smoothing mesh.
Smooth seconds: 1.55
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.12
Total running seconds: 29.23
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 161090
Mesh tetrahedra: 983422
Mesh faces: 1986452
Mesh subfaces: 39216
Mesh subsegments: 672
mesh nodes = 161090 mesh elts = 983422
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.155 seconds element count = 646614
count inserted = 200000 elapsed = 0.249 seconds element count = 1962807
count inserted = 300000 elapsed = 0.251 seconds element count = 3328011
count inserted = 400000 elapsed = 0.213 seconds element count = 4605475
count inserted = 500000 elapsed = 0.19 seconds element count = 5816937
count inserted = 600000 elapsed = 0.178 seconds element count = 7021117
count inserted = 700000 elapsed = 0.163 seconds element count = 8221554
count inserted = 800000 elapsed = 0.16 seconds element count = 9414930
count inserted = 900000 elapsed = 0.151 seconds element count = 10618043
done building octree - total elements = 11627886
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 148601
Total BCs = 548640
no-eqs = 483270
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=483270, cols=483270
total: nonzeros=22403274, allocated nonzeros=22403589
using I-node routines: found 161106 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=483270, cols=483270
total: nonzeros=22403274, allocated nonzeros=22403589
using I-node routines: found 161106 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 159986
countInvalid = 0 general-count = 548640
Average of the error norm = 0.220278
Initial error = 0.517031
Average of the error norm conditional = 0.21357
Active Residual error = 0.0578494
Total error = 0.220278
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 161831
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 531
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 176091
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 549
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 185770
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 591
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_9
Initial transform
name = compressed_step_10
Initial transform
name = compressed_step_11
Initial transform
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 4.32501
Max after displacement = 23.7541
Error points = 0
======================
step = 8
===============
elt_vol= 7.1875
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.04
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 28.88
Smoothing mesh.
Smooth seconds: 1.61
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.13
Total running seconds: 30.68
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 167900
Mesh tetrahedra: 1025838
Mesh faces: 2071897
Mesh subfaces: 40442
Mesh subsegments: 681
mesh nodes = 167900 mesh elts = 1025838
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.153 seconds element count = 626439
count inserted = 200000 elapsed = 0.242 seconds element count = 1900150
count inserted = 300000 elapsed = 0.244 seconds element count = 3235861
count inserted = 400000 elapsed = 0.208 seconds element count = 4488148
count inserted = 500000 elapsed = 0.189 seconds element count = 5675014
count inserted = 600000 elapsed = 0.172 seconds element count = 6850007
count inserted = 700000 elapsed = 0.161 seconds element count = 8020237
count inserted = 800000 elapsed = 0.157 seconds element count = 9189052
count inserted = 900000 elapsed = 0.147 seconds element count = 10361741
count inserted = 1000000 elapsed = 0.139 seconds element count = 11543327
done building octree - total elements = 11851384
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 150554
Total BCs = 548640
no-eqs = 503700
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
after setup_load_mfc
Linear solve converged due to CONVERGED_ITS iterations 1
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=503700, cols=503700
total: nonzeros=23361666, allocated nonzeros=23361981
using I-node routines: found 167916 nodes, limit used is 5
convergence reason = 4
KSP Object:
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-09, absolute=1e-50, divergence=10000
left preconditioning
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=seqaij, rows=503700, cols=503700
total: nonzeros=23361666, allocated nonzeros=23361981
using I-node routines: found 167916 nodes, limit used is 5
Iterations 1
Absolute-Norm of error = 170772
countInvalid = 1 general-count = 548639
Average of the error norm = 0.243825
Initial error = 0.540617
Average of the error norm conditional = 0.233757
Active Residual error = 0.0641518
Total error = 0.243827
c0324 time elapsed updating the sources (seconds) = 0
orientation_pbs
solving topology problems
using old topology solver
using Lame constants given by
E = 1000
nu = 0.3
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 175909
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 528
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 223243
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 759
DirectSolverConvergence = ksp-converged-rtol
btest = 1
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
done building octree - total elements = 158212
solving cropped problem
computing statistics for the displacement application error
average norm of error in placement = 0
LOAD size = 489
DirectSolverConvergence = ksp-converged-rtol
btest = 1
before
after
!!!! No residual problems.
DONE
compressing morph
dcds mesh direct image = 0 0 0
dir img for computed transform = 6.95251e-310 6.95251e-310 6.44056e-315
dir img for compressed = 6.95251e-310 6.95251e-310 6.44056e-315
dcds total image for source point = 6.95251e-310 6.95251e-310 6.44056e-315
name = compressed_step_8
Initial transform
name = compressed_step_9
Initial transform
name = compressed_step_10
Initial transform
name = compressed_step_11
Initial transform
name = compressed_step_12
Initial transform
name = compressed_step_13
Initial transform
name = compressed_step_14
Initial transform
name = compressed_step_15
Initial transform
name = compressed_step_16
Initial transform
name = compressed_step_17
Initial transform
name =
FEM error
Initial displacement = 7.37233
Final displacement = 3.99804
Max after displacement = 22.8115
Error points = 0
======================
step = 7
===============
elt_vol= 6.875
Constructing Delaunay tetrahedralization.
Delaunay seconds: 0
Creating surface mesh.
Perturbing vertices.
Delaunizing segments.
Constraining facets.
Segment and facet seconds: 0.05
Removing unwanted tetrahedra.
Hole seconds: 0
Repairing mesh.
Repair seconds: 0
Adding Steiner points to enforce quality.
Quality seconds: 31.5
Smoothing mesh.
Smooth seconds: 1.79
Writing nodes.
Writing elements.
Writing faces.
Output seconds: 0.14
Total running seconds: 33.5
Statistics:
Input points: 8
Input facets: 6
Input holes: 0
Input regions: 0
Mesh points: 175381
Mesh tetrahedra: 1072657
Mesh faces: 2166120
Mesh subfaces: 41612
Mesh subsegments: 688
mesh nodes = 175381 mesh elts = 1072657
building index src
done building the list
count inserted = 0 elapsed = 0 seconds element count = 1
count inserted = 100000 elapsed = 0.154 seconds element count = 604071
count inserted = 200000 elapsed = 0.248 seconds element count = 1842474
count inserted = 300000 elapsed = 0.254 seconds element count = 3143974
count inserted = 400000 elapsed = 0.217 seconds element count = 4371484
count inserted = 500000 elapsed = 0.192 seconds element count = 5532322
count inserted = 600000 elapsed = 0.175 seconds element count = 6679323
count inserted = 700000 elapsed = 0.165 seconds element count = 7818280
count inserted = 800000 elapsed = 0.166 seconds element count = 8959283
count inserted = 900000 elapsed = 0.153 seconds element count = 10100021
count inserted = 1000000 elapsed = 0.151 seconds element count = 11248357
done building octree - total elements = 12086420
penalty_weight = 1000
setting bc 205.891 174.948 225.515 -> 0 0 0
instead 205.881 174.938 225.505 -> norm = 0.0173205
setting bc 205.891 174.948 27.6148 -> 0 0 0
instead 205.881 174.938 27.6248 -> norm = 0.0173205
setting bc 205.891 35.1985 225.515 -> 0 0 0
instead 205.881 35.2085 225.505 -> norm = 0.0173205
setting bc 205.891 35.1985 27.6148 -> 0 0 0
instead 205.881 35.2085 27.6248 -> norm = 0.0173205
setting bc 52.3002 174.948 225.515 -> 0 0 0
instead 52.3102 174.938 225.505 -> norm = 0.0173205
setting bc 52.3002 174.948 27.6148 -> 0 0 0
instead 52.3102 174.938 27.6248 -> norm = 0.0173205
setting bc 52.3002 35.1985 225.515 -> 0 0 0
instead 52.3102 35.2085 225.505 -> norm = 0.0173205
setting bc 52.3002 35.1985 27.6148 -> 0 0 0
instead 52.3102 35.2085 27.6248 -> norm = 0.0173205
computing statistics for the displacement application error
average norm of error in placement = 0.0173205
iterating
done with candidates
Active BCs = 153450
Total BCs = 548640
no-eqs = 526143
percentage done= 0
percentage done= 5
percentage done= 10
percentage done= 15
percentage done= 20
percentage done= 25
percentage done= 30
percentage done= 35
percentage done= 40
percentage done= 45
percentage done= 50
percentage done= 55
percentage done= 60
percentage done= 65
percentage done= 70
percentage done= 75
percentage done= 80
percentage done= 85
percentage done= 90
percentage done= 95
done_bc_natural size of container = 548640
after building the map
LOAD size = 24
mri_cvs_register: Step 2 (elastic registration) took 780 seconds
applyMorph --template /usr/local/freesurfer/subjects//cvs_avg35/mri//aseg.mgz --transform /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35.tm3d vol /media/drivee/subjects/RETU/mri//aseg.mgz /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35_aseg.mgz nearest
Template name:/usr/local/freesurfer/subjects//cvs_avg35/mri//aseg.mgz
After loading template
Template name:/usr/local/freesurfer/subjects//cvs_avg35/mri//aseg.mgz
After loading template
extension = tm3d
Exception caught while loading transform
VolumeMorph load - failed to open input stream
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