External Email - Use Caution
Hi Marie,
The error message "Killed" is usually thrown when the device runs out of
memory. Can you double-check that this is not the case? If you're on Ubuntu
you can track your memory usage with the command ("htop" or "top").
The SAMSEG log you provided looks good to me.
Stefano
[Freesurfer] run_samseg: Optimizer: maximalDeformation is too small;
stopping; killed
<https://secure-web.cisco.com/114ojuev3dL_eHg7uTGqpjYcYMhO6cH4mJbsWSMTEvEouddqhXxUv3rQeSovxgzaRqpcJ6iXWgDdmd8D4Gc_OB_YC8DncH9hgXUOFHOgfTMn94uZpbzl7ip6S0YvhBvUx1lHQUwbhXas1ZB9Fne7_S1pUioWcpOWU8XlUJwCopZQTUDKbblRbIVG2nbOYJLY_Ef8HMyKskjyPjBgoWl1lz4WXD5o_cD5g2fyDVjcpQjQvixD5SB-AMLXvWEUhZfdZ5XFf5dhQMMOohPr7BKwzWZpj1lZYlmPf5jTQJFS4AbBE2lQEUAOcp8sEj29AU3HoP1yPLRm28iauLTX2M70nQw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Brun_samseg%255C%253A%2BOptimizer%255C%253A%2BmaximalDeformation%2Bis%2Btoo%2Bsmall%253B%2Bstopping%253B%2Bkilled%2522%26o%3Dnewest>
Ringki Marie Siewert
<https://secure-web.cisco.com/1K89zJlQ6eJrrX8555rwKUHZ19K0pqU4fGS0TjTv5M7vUgnEqGJJ4nCVM085Q8UtoN3yf-wsMBwMO45zydeI9SxrXZXy5GzWci2W8eQZr0NeLELjrGMmtlQJ88QEpw16ucrVWpvujn_kvqiGHDj6XW_uVbFmjGiUtteIKxTYCzfETlnKIbAJ73oI4uDiKmclU84py1J-PomYVvCooKfCrbs4sOXJAlf1rz0EiK2KhrB6LLCKwaLP2_HEImrwFBFey-5Q8VndrlWNGeRPo0xDzGqzgfEQoz2zvbN7GbKbRPm2vg0XKmiz3hiOURbj6TQr7SqhrE-X9453jIbI1WsiKKg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Ringki%2BMarie%2BSiewert%2522>
Wed, 22 May 2024 11:04:52 -0700
<https://secure-web.cisco.com/1kCmJa4nr649UKj0FFzt1TncfWCWs2wpdsUwdZgFIudtKezL4B7cEfKhXtQOrvfIw2Bl0jGgZECQ0kUDF6bLNig8BxEYtX8zb7OBqjeKYIgZu4a62NQuFK5LCYrF41uT5ugm7XghOGmuPBfRRdF5J3LbuHF3Ef3Z6ovfE2FFOxaay70ANYB6Y7dYDWsPtIFwy6Xd3E4100WMGIOSY3ZJjo-d3CIgVi7gggSkElu33YTK9RhlqVE64ixv5r_ldW3sm3wk4DI7gCT0XmpzUaPgo9aA0s6nRnQeUknSWV-0i_5snF7wC_LX3eAJysH1K_g2Yuqy2X6XSrB1OwUQG784iJw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20240522>
External Email - Use Caution
Hello Freesurfer Developers,
I'm a medical student training with Freesurfer for my doctor thesis. My
goal is to measure the brain volumetry of patients via SAMSEG. Attached is
my logfile for run_samseg.
When i run the samseg command:
run_samseg --input STRUCT_samseg.nii.gz --output
~/fsl_course_data/registrat/SamsegOutput --threads 3
where: STRUCT_samseg.nii.gz is a T1 w image of a normal human brain.
It runs for a while an then gives me the message:
*Optimizer: maximalDeformation is too small; stopping*
*iterationNumber: 0*
*Killed*
and just stops. There the files created as samseg output:
samseg.talairach.lta template_coregistered.mgz
cost.txt template.lta template_transforms.mat,
but not the stats file that estimates the volumetry of the brain.
I've searched the forum but there weren't any similiar reports for this
error.
1) FreeSurfer
version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
2) Plattform: Ubuntu 20.04.6 LTS
3) uname -a: Linux TABLET-TSKI5C88 5.15.146.1-microsoft-standard-WSL2 #1
SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
4) log as text file is attached
Last but not least I want to thank you for all your hard work!
I really appreciate all the advice and support you give.
Have a nice day,
Marie
Script started on 2024-05-22 15:06:09+02:00 [TERM="xterm-256color"
TTY="/dev/pts/0" COLUMNS="72" LINES="46"]
-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni
FSL_DIR /home/ringki/fsl
]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput
[01;32mringki@TABLET-TSKI5C88 [00m:
[01;34m~/fsl_course_data/registration/SamsegOutput [00m$
run_samseg --input STRUCT_samseg.nii.gz --output
~/fsl_course_data/registration/
[A [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C
[C [C [C [C [C [C [C [C [C [C
SamsegOutput --threads 3
##----------------------------------------------
Samsegment Options
##----------------------------------------------
output directory: /home/ringki/fsl_course_data/registration/SamsegOutput
input images: STRUCT_samseg.nii.gz
modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259,
3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51,
62, 58, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName':
'/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz',
'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF',
'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle',
'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex',
'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter',
'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter',
'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus',
'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus',
'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC',
'3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen',
'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities',
'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle',
'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum',
'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'],
'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159,
176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42,
204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255],
[220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245,
255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220,
216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255],
[196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42,
255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13,
176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [200, 70, 255, 255], [120,
18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255],
[122, 186, 220, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 220,
255], [0, 118, 14, 255], [164, 108, 226, 255], [120, 190, 150, 255]],
'sharedGMMParameters': [GMMparameter(mergedName='Unknown',
numberOfComponents=1, searchStrings=['Unknown', 'Skull']),
GMMparameter(mergedName='GlobalWM', numberOfComponents=1,
searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus',
'Pallidum']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1,
searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens',
'hypointensities', 'Thalamus']), GMMparameter(mergedName='GlobalCSF_messy',
numberOfComponents=1, searchStrings=['CSF', 'vessel', 'choroid-plexus',
'Fluid']), GMMparameter(mergedName='GlobalCSF_clean', numberOfComponents=1,
searchStrings=['Ventricle', 'Inf-Lat-Vent', 'Fluid']),
GMMparameter(mergedName='Putamen', numberOfComponents=1,
searchStrings=['Putamen']), GMMparameter(mergedName='Soft',
numberOfComponents=3, searchStrings=['Soft'])],
'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5,
'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50,
'whiteMatterAndCortexSmoothingSigma': 0}
optimizationOptions: {'maximumNumberOfDeformationIterations': 20,
'absoluteCostPerVoxelDecreaseStopCriterion': 0.0001, 'verbose': False,
'maximalDeformationStopCriterion': 0.001,
'lineSearchMaximalDeformationIntervalStopCriterion': 0.001,
'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12,
'multiResolutionSpecification': [{'atlasFileName':
'/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz',
'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 100,
'estimateBiasField': True}, {'atlasFileName':
'/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz',
'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 100,
'estimateBiasField': True}]}
Constructing image-to-world transform from header information
(STRUCT_samseg.nii.gz)
Read image: STRUCT_samseg.nii.gz
Constructing image-to-world transform from header information
(/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii)
Read image:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii
performing affine atlas registration
image: STRUCT_samseg.nii.gz
template:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz
Transforming points
Transforming points
AFFINE
min: 0
max: 644
robustMin: 0
robustMax: 514.041
histogram[ 0 ]: 14882
histogram[ 1 ]: 0
histogram[ 2 ]: 0
histogram[ 3997 ]: 0
histogram[ 3998 ]: 0
histogram[ 3999 ]: 1
cumulativeHistogram[ 0 ]: 0.0422477
cumulativeHistogram[ 1 ]: 0.0422477
cumulativeHistogram[ 2 ]: 0.0422477
cumulativeHistogram[ 3997 ]: 0.999997
cumulativeHistogram[ 3998 ]: 0.999997
cumulativeHistogram[ 3999 ]: 1
AFFINE
min: 0
max: 644
robustMin: 0
robustMax: 514.041
histogram[ 0 ]: 14882
histogram[ 1 ]: 0
histogram[ 2 ]: 0
histogram[ 3997 ]: 0
histogram[ 3998 ]: 0
histogram[ 3999 ]: 1
cumulativeHistogram[ 0 ]: 0.0422477
cumulativeHistogram[ 1 ]: 0.0422477
cumulativeHistogram[ 2 ]: 0.0422477
cumulativeHistogram[ 3997 ]: 0.999997
cumulativeHistogram[ 3998 ]: 0.999997
cumulativeHistogram[ 3999 ]: 1
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz
Transforming points
Transforming points
AFFINE
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.005
MaximalDeformationStopCriterion: 0.005
Verbose: 0
min: 0
max: 644
robustMin: 0
robustMax: 514.041
histogram[ 0 ]: 14882
histogram[ 1 ]: 0
histogram[ 2 ]: 0
histogram[ 3997 ]: 0
histogram[ 3998 ]: 0
histogram[ 3999 ]: 1
cumulativeHistogram[ 0 ]: 0.0422477
cumulativeHistogram[ 1 ]: 0.0422477
cumulativeHistogram[ 2 ]: 0.0422477
cumulativeHistogram[ 3997 ]: 0.999997
cumulativeHistogram[ 3998 ]: 0.999997
cumulativeHistogram[ 3999 ]: 1
maximalDeformation=1.0000 minLogLikelihood=-0.7611
maximalDeformation=1.6862 minLogLikelihood=-0.7777
maximalDeformation=1.4750 minLogLikelihood=-0.7945
maximalDeformation=1.2925 minLogLikelihood=-0.8050
maximalDeformation=0.9504 minLogLikelihood=-0.8100
maximalDeformation=1.0036 minLogLikelihood=-0.8131
maximalDeformation=0.2880 minLogLikelihood=-0.8143
maximalDeformation=0.0198 minLogLikelihood=-0.8143
maximalDeformation=0.0000 minLogLikelihood=-0.8143
appliedScaling: 1.0160
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz
Transforming points
Transforming points
AFFINE
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.005
MaximalDeformationStopCriterion: 0.005
Verbose: 0
min: 0
max: 644
robustMin: 0
robustMax: 514.041
histogram[ 0 ]: 14882
histogram[ 1 ]: 0
histogram[ 2 ]: 0
histogram[ 3997 ]: 0
histogram[ 3998 ]: 0
histogram[ 3999 ]: 1
cumulativeHistogram[ 0 ]: 0.0422477
cumulativeHistogram[ 1 ]: 0.0422477
cumulativeHistogram[ 2 ]: 0.0422477
cumulativeHistogram[ 3997 ]: 0.999997
cumulativeHistogram[ 3998 ]: 0.999997
cumulativeHistogram[ 3999 ]: 1
maximalDeformation=1.0000 minLogLikelihood=-0.8302
maximalDeformation=0.2745 minLogLikelihood=-0.8304
maximalDeformation=0.0976 minLogLikelihood=-0.8304
maximalDeformation=0.0656 minLogLikelihood=-0.8306
maximalDeformation=0.1658 minLogLikelihood=-0.8309
maximalDeformation=0.0092 minLogLikelihood=-0.8309
maximalDeformation=0.0000 minLogLikelihood=-0.8309
appliedScaling: 1.0033
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz
Transforming points
Transforming points
AFFINE
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.005
MaximalDeformationStopCriterion: 0.005
Verbose: 0
min: 0
max: 644
robustMin: 0
robustMax: 514.041
histogram[ 0 ]: 14882
histogram[ 1 ]: 0
histogram[ 2 ]: 0
histogram[ 3997 ]: 0
histogram[ 3998 ]: 0
histogram[ 3999 ]: 1
cumulativeHistogram[ 0 ]: 0.0422477
cumulativeHistogram[ 1 ]: 0.0422477
cumulativeHistogram[ 2 ]: 0.0422477
cumulativeHistogram[ 3997 ]: 0.999997
cumulativeHistogram[ 3998 ]: 0.999997
cumulativeHistogram[ 3999 ]: 1
maximalDeformation=0.7196 minLogLikelihood=-0.8348
maximalDeformation=0.0000 minLogLikelihood=-0.8348
appliedScaling: 1.0014
writing template transform to
/home/ringki/fsl_course_data/registration/SamsegOutput/template.lta
writing talairach transform to
/home/ringki/fsl_course_data/registration/SamsegOutput/samseg.talairach.lta
atlas registration complete: 0:00:25.938044
Constructing image-to-world transform from header information
(STRUCT_samseg.nii.gz)
Read image: STRUCT_samseg.nii.gz
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Transforming points
Transforming points
[1.015625 1.015625 1. ]
Unknown
Unknown (100%)
Skull (100%)
GlobalWM
Brain-Stem (100%)
Left-Cerebellum-White-Matter (100%)
Right-Cerebellum-White-Matter (100%)
Right-Cerebral-White-Matter (100%)
Left-Cerebral-White-Matter (100%)
Optic-Chiasm (100%)
Right-VentralDC (100%)
Left-VentralDC (100%)
Right-Pallidum (100%)
Right-Thalamus (50%)
Left-Pallidum (100%)
Left-Thalamus (50%)
GlobalGM
Left-Cerebellum-Cortex (100%)
Right-Cerebellum-Cortex (100%)
Left-Cerebral-Cortex (100%)
Right-Cerebral-Cortex (100%)
Right-Amygdala (100%)
Left-Amygdala (100%)
Right-Hippocampus (100%)
Left-Hippocampus (100%)
Left-Accumbens-area (100%)
Right-Accumbens-area (100%)
WM-hypointensities (100%)
Left-Caudate (100%)
Right-Thalamus (50%)
Right-Caudate (100%)
Left-Thalamus (50%)
non-WM-hypointensities (100%)
GlobalCSF_messy
CSF (100%)
Fluid_Inside_Eyes (50%)
Right-choroid-plexus (100%)
Left-choroid-plexus (100%)
Right-vessel (100%)
Left-vessel (100%)
GlobalCSF_clean
4th-Ventricle (100%)
Fluid_Inside_Eyes (50%)
Right-Inf-Lat-Vent (100%)
Left-Inf-Lat-Vent (100%)
3rd-Ventricle (100%)
Left-Lateral-Ventricle (100%)
Right-Lateral-Ventricle (100%)
5th-Ventricle (100%)
Putamen
Left-Putamen (100%)
Right-Putamen (100%)
Soft
Soft_Nonbrain_Tissue (100%)
====================
{
depth: 1
maximumNumberOfDeformationIterations: 20
absoluteCostPerVoxelDecreaseStopCriterion: 0.0001
verbose: False
maximalDeformationStopCriterion: 0.001
lineSearchMaximalDeformationIntervalStopCriterion: 0.001
maximalDeformationAppliedStopCriterion: 0.0
BFGSMaximumMemoryLength: 12
multiResolutionSpecification: {
depth: 2
atlasFileName:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz
targetDownsampledVoxelSpacing: 2.0
maximumNumberOfIterations: 100
estimateBiasField: True
}, {
depth: 2
atlasFileName:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
targetDownsampledVoxelSpacing: 1.0
maximumNumberOfIterations: 100
estimateBiasField: True
}
}
====================
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz
Transforming points
Transforming points
iterationNumber: 0
EM converged!
1
0.398942
SLIDING
FutureWarning: The default value of `n_init` will change from 10 to 'auto' in
1.4. Set the value of `n_init` explicitly to suppress the warning
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 0
efficiency: 126.7000 %
relative size: 24.6395 %
setup time: 1.2095 sec
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 1
efficiency: 128.3933 %
relative size: 20.0000 %
setup time: 0.6145 sec
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 2
efficiency: 127.1974 %
relative size: 18.9204 %
setup time: 0.6081 sec
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 3
efficiency: 122.7357 %
relative size: 19.8431 %
setup time: 0.5968 sec
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 4
efficiency: 127.1474 %
relative size: 19.2977 %
setup time: 0.6058 sec
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.001
MaximalDeformationStopCriterion: 0.001
MaximumNumberOfIterations: 20
Verbose: 0
blockNumber 5
efficiency: 126.6879 %
relative size: 23.7617 %
setup time: 0.6279 sec
Total time spent: 1.3786 sec
maximalDeformation=2.3455
Total time spent: 1.1736 sec
maximalDeformation=1.3181
Total time spent: 1.1150 sec
maximalDeformation=0.9837
Total time spent: 0.0030 sec
maximalDeformation=0.0000
maximalDeformationApplied: 2.7207
=======================================================
iterationNumber: 1
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.3099 sec
maximalDeformation=0.9719
Total time spent: 1.3018 sec
maximalDeformation=1.1376
Total time spent: 1.0990 sec
maximalDeformation=1.0771
Total time spent: 0.0031 sec
maximalDeformation=0.0000
maximalDeformationApplied: 1.8142
=======================================================
iterationNumber: 2
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.4168 sec
maximalDeformation=0.9816
Total time spent: 1.2834 sec
maximalDeformation=0.7318
Total time spent: 1.0291 sec
maximalDeformation=0.8476
Total time spent: 0.0031 sec
maximalDeformation=0.0000
maximalDeformationApplied: 1.9384
=======================================================
iterationNumber: 3
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.3210 sec
maximalDeformation=0.7104
Total time spent: 1.0347 sec
maximalDeformation=0.8439
Total time spent: 0.9609 sec
maximalDeformation=0.5982
Total time spent: 0.0037 sec
maximalDeformation=0.0000
maximalDeformationApplied: 1.7072
=======================================================
iterationNumber: 4
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.2096 sec
maximalDeformation=0.8494
Total time spent: 1.0121 sec
maximalDeformation=0.7369
Total time spent: 0.9503 sec
maximalDeformation=0.9738
Total time spent: 0.0030 sec
maximalDeformation=0.0000
maximalDeformationApplied: 2.1911
=======================================================
iterationNumber: 5
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.2341 sec
maximalDeformation=0.8784
Total time spent: 1.0890 sec
maximalDeformation=0.6860
Total time spent: 0.9218 sec
maximalDeformation=0.9306
Total time spent: 0.0028 sec
maximalDeformation=0.0000
maximalDeformationApplied: 2.3352
=======================================================
iterationNumber: 6
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.1320 sec
maximalDeformation=0.8858
Total time spent: 1.0573 sec
maximalDeformation=0.7423
Total time spent: 1.0033 sec
maximalDeformation=0.5425
Total time spent: 0.0033 sec
maximalDeformation=0.0000
maximalDeformationApplied: 1.8393
=======================================================
iterationNumber: 7
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.0969 sec
maximalDeformation=0.4317
Total time spent: 1.0330 sec
maximalDeformation=0.2635
Total time spent: 0.8456 sec
maximalDeformation=0.2330
Total time spent: 0.0031 sec
maximalDeformation=0.0000
maximalDeformationApplied: 0.7037
=======================================================
iterationNumber: 8
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.1469 sec
maximalDeformation=0.1336
Total time spent: 0.9835 sec
maximalDeformation=0.1533
Total time spent: 0.9917 sec
maximalDeformation=0.0903
Total time spent: 0.0038 sec
maximalDeformation=0.0000
maximalDeformationApplied: 0.2659
=======================================================
iterationNumber: 9
EM converged!
1
0.398942
SLIDING
ProbabilisticAtlas reusing warm optimizers!!
Total time spent: 1.1334 sec
maximalDeformation=0.0820
Total time spent: 1.0976 sec
maximalDeformation=0.1198
Total time spent: 0.8241 sec
maximalDeformation=0.1144
Total time spent: 0.0030 sec
maximalDeformation=0.0000
maximalDeformationApplied: 0.2500
=======================================================
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Transforming points
Transforming points
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz
Read mesh collection:
/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
SLIDING
L-BFGS
BFGS-MaximumMemoryLength: 12
LineSearchMaximalDeformationIntervalStopCriterion: 0.005
MaximalDeformationStopCriterion: 0.005
Verbose: 1
[BRACKETING] Found a really good solution -- no need for zooming: 1
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 7.16011
-----------------------
[BRACKETING] Hit a really bad solution -- ready for zooming: 3.55517
[ZOOMING] Zooming with low=0 and high=3.55517
bisected: 1.77758
[ZOOMING] Found a good solution: 1.77758
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 1.33934
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.132102
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.109576
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.0715406
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.0258653
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.0195591
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.0061019
-----------------------
[BRACKETING] Found a really good solution -- no need for zooming: 0.00454179
-----------------------
Optimizer: maximalDeformation is too small; stopping
iterationNumber: 0
Killed
]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput
[01;32mringki@TABLET-TSKI5C88 [00m:
[01;34m~/fsl_course_data/registration/SamsegOutput [00m$
]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput
[01;32mringki@TABLET-TSKI5C88 [00m:
[01;34m~/fsl_course_data/registration/SamsegOutput [00m$
exit
exit
Script done on 2024-05-22 15:10:40+02:00 [COMMAND_EXIT_CODE="137"]
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