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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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Workflow issue #644

Closed vnckppl closed 6 years ago

vnckppl commented 6 years ago

Hi mriqc devs,

I am running MRIQC in docker (stable; Version 17.06.2-ce-mac27 (19124)) on OSX 10.11.16.

I started mriqc with the following command:

docker run \
       -it \
       --rm \
       -v "${ddir}":/data:ro \
       -v "${odir}":/out poldracklab/mriqc:latest /data /out participant \
       --participant_label sub-CF1036ENT sub-CF1038ENT sub-CF1051ENT

(where ddir is my data folder and odir is my output folder)

Mriqc does not finish, but crashes. Here is the terminal output:

Unable to find image 'poldracklab/mriqc:latest' locally
latest: Pulling from poldracklab/mriqc
b3e1c725a85f: Pull complete
4daad8bdde31: Pull complete
63fe8c0068a8: Pull complete
4a70713c436f: Pull complete
bd842a2105a8: Pull complete
230426d0ba20: Pull complete
769712fb8ed6: Pull complete
df5d156c1bd6: Pull complete
a3ed95caeb02: Pull complete
7d168d5683fe: Pull complete
b4d42920f990: Pull complete
9566450a8e0d: Pull complete
2e3cf2618532: Pull complete
ad5f3825b1ec: Pull complete
dde2d4a18558: Pull complete
0aa4b78bf26e: Pull complete
274f71ab638e: Pull complete
76ceae0b80a4: Pull complete
7682485137cb: Pull complete
a1db59af86d9: Pull complete
12ee24f49996: Pull complete
c67e0250398b: Pull complete
a82d21f8894e: Pull complete
63c87dc7f490: Pull complete
Digest: sha256:94b70fe33b24f60c814003872cb4e536c9c5b497697753e8e8f75b8d5b0005b8
Status: Downloaded newer image for poldracklab/mriqc:latest
**mriqc v0.9.8-1**
2017-09-18 17:40:33,949 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-5~nd16.04+1 and AFNI_17.2.13 is available.
2017-09-18 17:40:34,350 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-5~nd16.04+1 and AFNI_17.2.13 is available.
2017-09-18 17:40:34,479 mriqc.cli:WARNING No bold scans were found in /data
2017-09-18 17:40:34,479 mriqc.cli:WARNING No T2w scans were found in /data
2017-09-18 17:40:34,479 mriqc.cli:WARNING Anonymized quality metrics will be submitted to MRIQC's metrics repository. Use --no-sub to disable submission.
2017-09-18 17:42:20,680 niworkflows:INFO Estimating initial transform using AffineInitializer
2017-09-18 17:42:43,161 niworkflows:INFO Estimating initial transform using AffineInitializer
2017-09-18 17:44:05,936 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.6/site-packages/niworkflows/data/t1-mni_registration_fast_000.json.
2017-09-18 17:44:06,020 niworkflows:INFO Retry #0, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1
2017-09-18 17:44:11,601 workflow:ERROR ['Node segmentation.a0 failed to run on host 8bb44527869c.']
2017-09-18 17:44:23,128 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.6/site-packages/niworkflows/data/t1-mni_registration_fast_000.json.
2017-09-18 17:44:23,193 niworkflows:INFO Retry #0, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1
2017-09-18 17:45:30,976 niworkflows:WARNING Retry #0 failed: Command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz, /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1
Standard output:
All_Command_lines_OK
Using double precision for computations.
=============================================================================
The composite transform comprises the following transforms (in order):
1. /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/transform.mat (type = AffineTransform)
=============================================================================
number of levels = 1
number of levels = 3
number of levels = 2
fixed image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz
moving image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz
fixed image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz
moving image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz
fixed image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz
moving image: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1038ENT..anat..sub-CF1038ENT_T1w.nii/SpatialNormalization/moving_masked.nii.gz
Dimension = 3
Number of stages = 3
Use Histogram Matching true
Winsorize image intensities true
Lower quantile = 0
Upper quantile = 1
Stage 1 State
Image metric = Mattes
Fixed image = Image (0x498b500)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1401
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 1223
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
Spacing: [2, 2, 2]
Origin: [96.5, 132.5, -78.5]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-2 0 0
0 -2 0
0 0 2

PointToIndexMatrix:
-0.5 0 0
0 -0.5 0
0 0 0.5

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x4975a00)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1220
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f958f923010
Container manages memory: true
Size: 1082035
Capacity: 1082035

Moving image = Image (0x498e670)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1402
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 1399
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
Spacing: [0.9375, 0.9375, 1.5]
Origin: [119.532, 110.165, -64.7015]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-0.9375 0 0
0 -0.9375 0
0 0 1.5

PointToIndexMatrix:
-1.06667 0 0
0 -1.06667 0
0 0 0.666667

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x498e980)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1396
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f958c422010
Container manages memory: true
Size: 6946816
Capacity: 6946816

Weighting = 1
Sampling strategy = random
Number of bins = 32
Radius = 4
Sampling percentage  = 0.15
Transform = Rigid
Gradient step = 0.01
Update field sigma (voxel space) = 0
Total field sigma (voxel space) = 0
Update field time sigma = 0
Total field time sigma  = 0
Number of time indices = 0
Number of time point samples = 0
Stage 2 State
Image metric = Mattes
Fixed image = Image (0x4992880)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1755
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 1577
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
Spacing: [2, 2, 2]
Origin: [96.5, 132.5, -78.5]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-2 0 0
0 -2 0
0 0 2

PointToIndexMatrix:
-0.5 0 0
0 -0.5 0
0 0 0.5

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x4992b40)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1574
Debug: Off
Object Name:
Observers:
none
Pointer: 0x49991a0
Container manages memory: true
Size: 1082035
Capacity: 1082035

Moving image = Image (0x498cd30)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1756
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 1753
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
Spacing: [0.9375, 0.9375, 1.5]
Origin: [119.532, 110.165, -64.7015]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-0.9375 0 0
0 -0.9375 0
0 0 1.5

PointToIndexMatrix:
-1.06667 0 0
0 -1.06667 0
0 0 0.666667

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x4998a60)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1750
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f9588f21010
Container manages memory: true
Size: 6946816
Capacity: 6946816

Weighting = 1
Sampling strategy = regular
Number of bins = 32
Radius = 4
Sampling percentage  = 0.15
Transform = Affine
Gradient step = 0.08
Update field sigma (voxel space) = 0
Total field sigma (voxel space) = 0
Update field time sigma = 0
Total field time sigma  = 0
Number of time indices = 0
Number of time point samples = 0
Stage 3 State
Image metric = Mattes
Fixed image = Image (0x498cff0)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 2109
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 1931
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [97, 115, 97]
Spacing: [2, 2, 2]
Origin: [96.5, 132.5, -78.5]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-2 0 0
0 -2 0
0 0 2

PointToIndexMatrix:
-0.5 0 0
0 -0.5 0
0 0 0.5

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x4995750)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1928
Debug: Off
Object Name:
Observers:
none
Pointer: 0x51e0bf0
Container manages memory: true
Size: 1082035
Capacity: 1082035

Moving image = Image (0x5a22190)
RTTI typeinfo:   itk::Image<double, 3u>
Reference Count: 2
Modified Time: 2110
Debug: Off
Object Name:
Observers:
none
Source: (none)
Source output name: (none)
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 2107
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [256, 256, 106]
Spacing: [0.9375, 0.9375, 1.5]
Origin: [119.532, 110.165, -64.7015]
Direction:
-1 0 0
0 -1 0
0 0 1

IndexToPointMatrix:
-0.9375 0 0
0 -0.9375 0
0 0 1.5

PointToIndexMatrix:
-1.06667 0 0
0 -1.06667 0
0 0 0.666667

Inverse Direction:
-1 0 0
0 -1 0
0 0 1

PixelContainer:
ImportImageContainer (0x51de340)
RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 2104
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f9585a20010
Container manages memory: true
Size: 6946816
Capacity: 6946816

Weighting = 1
Sampling strategy = regular
Number of bins = 56
Radius = 4
Sampling percentage  = 0.25
Transform = SyN
Gradient step = 0.1
Update field sigma (voxel space) = 3
Total field sigma (voxel space) = 0
Update field time sigma = 0
Total field time sigma  = 0
Number of time indices = 0
Number of time point samples = 0
Registration using 3 total stages.

Stage 0
iterations = 1000
convergence threshold = 1e-06
convergence window size = 20
number of levels = 1
using the Mattes MI metric (number of bins = 32, weight = 1)
preprocessing:  winsorizing the image intensities
preprocessing:  histogram matching the images
Shrink factors (level 1 out of 1): [4, 4, 4]
smoothing sigmas per level: [4]
random sampling (percentage = 0.15)

*** Running rigid registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC,     1, -1.000457139345e+00, 1.797693134862e+308, 2.7118e+00, 2.7118e+00,
2DIAGNOSTIC,     2, -1.000687231697e+00, 1.797693134862e+308, 2.7234e+00, 1.1632e-02,
2DIAGNOSTIC,     3, -1.001051444631e+00, 1.797693134862e+308, 2.7336e+00, 1.0131e-02,
2DIAGNOSTIC,     4, -1.001603442686e+00, 1.797693134862e+308, 2.7461e+00, 1.2585e-02,
2DIAGNOSTIC,     5, -1.002079213242e+00, 1.797693134862e+308, 2.7566e+00, 1.0411e-02,
2DIAGNOSTIC,     6, -1.002502136061e+00, 1.797693134862e+308, 2.7667e+00, 1.0174e-02,
2DIAGNOSTIC,     7, -1.003364883569e+00, 1.797693134862e+308, 2.7778e+00, 1.1061e-02,
2DIAGNOSTIC,     8, -1.004269862188e+00, 1.797693134862e+308, 2.7886e+00, 1.0823e-02,
2DIAGNOSTIC,     9, -1.005299023666e+00, 1.797693134862e+308, 2.7987e+00, 1.0103e-02,
2DIAGNOSTIC,    10, -1.005822106315e+00, 1.797693134862e+308, 2.8120e+00, 1.3269e-02,
2DIAGNOSTIC,    11, -1.005988578824e+00, 1.797693134862e+308, 2.8248e+00, 1.2854e-02,
2DIAGNOSTIC,    12, -1.005858784018e+00, 1.797693134862e+308, 2.8344e+00, 9.5170e-03,
2DIAGNOSTIC,    13, -1.006017579231e+00, 1.797693134862e+308, 2.8455e+00, 1.1161e-02,
2DIAGNOSTIC,    14, -1.006163930479e+00, 1.797693134862e+308, 2.8553e+00, 9.8341e-03,
2DIAGNOSTIC,    15, -1.006258229315e+00, 1.797693134862e+308, 2.8663e+00, 1.0970e-02,
2DIAGNOSTIC,    16, -1.006472211616e+00, 1.797693134862e+308, 2.8825e+00, 1.6159e-02,
2DIAGNOSTIC,    17, -1.006581789558e+00, 1.797693134862e+308, 2.8954e+00, 1.2909e-02,
2DIAGNOSTIC,    18, -1.006587324803e+00, 1.797693134862e+308, 2.9064e+00, 1.0966e-02,
2DIAGNOSTIC,    19, -1.006340054482e+00, 1.797693134862e+308, 2.9229e+00, 1.6576e-02,
2DIAGNOSTIC,    20, -1.006597796497e+00, 2.047177731089e-04, 2.9385e+00, 1.5606e-02,
2DIAGNOSTIC,    21, -1.006598109627e+00, 1.748609270242e-04, 2.9493e+00, 1.0815e-02,
2DIAGNOSTIC,    22, -1.006598709312e+00, 1.451250567414e-04, 2.9623e+00, 1.2937e-02,
2DIAGNOSTIC,    23, -1.006600804906e+00, 1.168416606122e-04, 2.9755e+00, 1.3248e-02,
2DIAGNOSTIC,    24, -1.006604675689e+00, 9.147484485183e-05, 2.9943e+00, 1.8756e-02,
2DIAGNOSTIC,    25, -1.006605695882e+00, 6.862627753400e-05, 3.0381e+00, 4.3810e-02,
2DIAGNOSTIC,    26, -1.006605695872e+00, 4.804563844208e-05, 3.0813e+00, 4.3238e-02,
2DIAGNOSTIC,    27, -1.006605695872e+00, 3.226154387157e-05, 3.0955e+00, 1.4115e-02,
2DIAGNOSTIC,    28, -1.006605695872e+00, 2.134518617900e-05, 3.1087e+00, 1.3213e-02,
2DIAGNOSTIC,    29, -1.006605695872e+00, 1.576417744076e-05, 3.1256e+00, 1.6894e-02,
2DIAGNOSTIC,    30, -1.006605695872e+00, 1.271434632153e-05, 3.1387e+00, 1.3164e-02,
2DIAGNOSTIC,    31, -1.006605695872e+00, 1.035556420752e-05, 3.1508e+00, 1.2121e-02,
2DIAGNOSTIC,    32, -1.006605695872e+00, 7.278544599469e-06, 3.1636e+00, 1.2793e-02,
2DIAGNOSTIC,    33, -1.006605695872e+00, 4.884807804605e-06, 3.1768e+00, 1.3213e-02,
2DIAGNOSTIC,    34, -1.006605695872e+00, 3.114306853035e-06, 3.1898e+00, 1.2904e-02,
2DIAGNOSTIC,    35, -1.006605695872e+00, 1.732909479371e-06, 3.2012e+00, 1.1411e-02,
2DIAGNOSTIC,    36, -1.006605695872e+00, 1.246215169674e-06, 3.2137e+00, 1.2521e-02,
2DIAGNOSTIC,    37, -1.006605695872e+00, 1.198822652062e-06, 3.2271e+00, 1.3429e-02,
2DIAGNOSTIC,    38, -1.006605695872e+00, 1.162182133509e-06, 3.2410e+00, 1.3861e-02,
Elapsed time (stage 0): 4.0781e+00

Stage 1
iterations = 500x250x100
convergence threshold = 1.0000e-06
convergence window size = 20
number of levels = 3
using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
preprocessing:  winsorizing the image intensities
preprocessing:  histogram matching the images
Shrink factors (level 1 out of 3): [4, 4, 4]
Shrink factors (level 2 out of 3): [2, 2, 2]
Shrink factors (level 3 out of 3): [1, 1, 1]
smoothing sigmas per level: [4, 2, 0]
regular sampling (percentage = 1.5000e-01)

*** Running affine registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC,     1, -1.014395626830e+00, 1.797693134862e+308, 2.7327e+00, 2.7327e+00,
2DIAGNOSTIC,     2, -1.016601098294e+00, 1.797693134862e+308, 2.7447e+00, 1.1991e-02,
2DIAGNOSTIC,     3, -1.020599622011e+00, 1.797693134862e+308, 2.7571e+00, 1.2369e-02,
2DIAGNOSTIC,     4, -1.024982675930e+00, 1.797693134862e+308, 2.7695e+00, 1.2442e-02,
2DIAGNOSTIC,     5, -1.030420581068e+00, 1.797693134862e+308, 2.7826e+00, 1.3145e-02,
2DIAGNOSTIC,     6, -1.035694781024e+00, 1.797693134862e+308, 2.7975e+00, 1.4886e-02,
2DIAGNOSTIC,     7, -1.045715978161e+00, 1.797693134862e+308, 2.8159e+00, 1.8398e-02,
2DIAGNOSTIC,     8, -1.049822128684e+00, 1.797693134862e+308, 2.8277e+00, 1.1813e-02,
2DIAGNOSTIC,     9, -1.053765981111e+00, 1.797693134862e+308, 2.8425e+00, 1.4730e-02,
2DIAGNOSTIC,    10, -1.057496694663e+00, 1.797693134862e+308, 2.8570e+00, 1.4561e-02,
2DIAGNOSTIC,    11, -1.058375789942e+00, 1.797693134862e+308, 2.8717e+00, 1.4653e-02,
2DIAGNOSTIC,    12, -1.059724073111e+00, 1.797693134862e+308, 2.8873e+00, 1.5659e-02,
2DIAGNOSTIC,    13, -1.060997082942e+00, 1.797693134862e+308, 2.9094e+00, 2.2060e-02,
2DIAGNOSTIC,    14, -1.061169653452e+00, 1.797693134862e+308, 2.9239e+00, 1.4458e-02,
2DIAGNOSTIC,    15, -1.061544970392e+00, 1.797693134862e+308, 2.9389e+00, 1.5018e-02,
2DIAGNOSTIC,    16, -1.061900221204e+00, 1.797693134862e+308, 2.9565e+00, 1.7594e-02,
2DIAGNOSTIC,    17, -1.061967513258e+00, 1.797693134862e+308, 2.9808e+00, 2.4292e-02,
2DIAGNOSTIC,    18, -1.061992148479e+00, 1.797693134862e+308, 2.9975e+00, 1.6714e-02,
2DIAGNOSTIC,    19, -1.062064053622e+00, 1.797693134862e+308, 3.0149e+00, 1.7460e-02,
2DIAGNOSTIC,    20, -1.062108108378e+00, 1.460334847373e-03, 3.0335e+00, 1.8557e-02,
2DIAGNOSTIC,    21, -1.062186631919e+00, 1.206173704310e-03, 3.0585e+00, 2.5004e-02,
2DIAGNOSTIC,    22, -1.062214573058e+00, 9.607327066147e-04, 3.0762e+00, 1.7683e-02,
2DIAGNOSTIC,    23, -1.062261125765e+00, 7.379754823119e-04, 3.1026e+00, 2.6421e-02,
2DIAGNOSTIC,    24, -1.062280165291e+00, 5.408811212720e-04, 3.1183e+00, 1.5646e-02,
2DIAGNOSTIC,    25, -1.062019176933e+00, 3.742105821896e-04, 3.1364e+00, 1.8112e-02,
2DIAGNOSTIC,    26, -1.062054951384e+00, 2.381917001453e-04, 3.1565e+00, 2.0164e-02,
2DIAGNOSTIC,    27, -1.062070163892e+00, 1.574653381843e-04, 3.1720e+00, 1.5452e-02,
2DIAGNOSTIC,    28, -1.062075878795e+00, 9.841193977728e-05, 3.1943e+00, 2.2268e-02,
2DIAGNOSTIC,    29, -1.062078686380e+00, 5.943476081847e-05, 3.2184e+00, 2.4107e-02,
2DIAGNOSTIC,    30, -1.062079385336e+00, 3.871092485628e-05, 3.2356e+00, 1.7249e-02,
2DIAGNOSTIC,    31, -1.062082069603e+00, 2.209738629628e-05, 3.2551e+00, 1.9504e-02,
2DIAGNOSTIC,    32, -1.062085038711e+00, 1.168084484417e-05, 3.2747e+00, 1.9544e-02,
2DIAGNOSTIC,    33, -1.062087494831e+00, 6.937390308763e-06, 3.2946e+00, 1.9990e-02,
2DIAGNOSTIC,    34, -1.062089614042e+00, 2.961216740420e-06, 3.3140e+00, 1.9354e-02,
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC,     1, -7.767994523273e-01, 1.797693134862e+308, 4.5738e+00, 1.2598e+00,
2DIAGNOSTIC,     2, -7.776985408082e-01, 1.797693134862e+308, 4.6859e+00, 1.1215e-01,
2DIAGNOSTIC,     3, -7.789703280746e-01, 1.797693134862e+308, 4.7880e+00, 1.0205e-01,
2DIAGNOSTIC,     4, -7.808432468318e-01, 1.797693134862e+308, 4.8890e+00, 1.0101e-01,
2DIAGNOSTIC,     5, -7.837726318307e-01, 1.797693134862e+308, 4.9919e+00, 1.0296e-01,
2DIAGNOSTIC,     6, -7.866686624657e-01, 1.797693134862e+308, 5.0901e+00, 9.8207e-02,
2DIAGNOSTIC,     7, -7.897156405744e-01, 1.797693134862e+308, 5.2274e+00, 1.3729e-01,
2DIAGNOSTIC,     8, -7.899706756132e-01, 1.797693134862e+308, 5.3601e+00, 1.3267e-01,
2DIAGNOSTIC,     9, -7.902444859456e-01, 1.797693134862e+308, 5.4952e+00, 1.3510e-01,
2DIAGNOSTIC,    10, -7.907935448154e-01, 1.797693134862e+308, 5.6139e+00, 1.1866e-01,
2DIAGNOSTIC,    11, -7.912586861505e-01, 1.797693134862e+308, 5.7090e+00, 9.5146e-02,
2DIAGNOSTIC,    12, -7.913548312795e-01, 1.797693134862e+308, 5.8236e+00, 1.1456e-01,
2DIAGNOSTIC,    13, -7.913700743796e-01, 1.797693134862e+308, 5.9397e+00, 1.1616e-01,
2DIAGNOSTIC,    14, -7.913981783528e-01, 1.797693134862e+308, 6.0575e+00, 1.1782e-01,
2DIAGNOSTIC,    15, -7.913986779622e-01, 1.797693134862e+308, 6.1829e+00, 1.2533e-01,
2DIAGNOSTIC,    16, -7.913489798134e-01, 1.797693134862e+308, 6.3015e+00, 1.1868e-01,
2DIAGNOSTIC,    17, -7.913280969550e-01, 1.797693134862e+308, 6.4199e+00, 1.1837e-01,
2DIAGNOSTIC,    18, -7.913059104199e-01, 1.797693134862e+308, 6.5732e+00, 1.5324e-01,
2DIAGNOSTIC,    19, -7.913013810561e-01, 1.797693134862e+308, 6.6790e+00, 1.0585e-01,
2DIAGNOSTIC,    20, -7.912835674488e-01, 5.266983474077e-04, 6.7804e+00, 1.0137e-01,
2DIAGNOSTIC,    21, -7.912916317658e-01, 4.082199908561e-04, 6.8778e+00, 9.7418e-02,
2DIAGNOSTIC,    22, -7.913501135866e-01, 2.986841231513e-04, 6.9791e+00, 1.0135e-01,
2DIAGNOSTIC,    23, -7.915462492144e-01, 2.027317681240e-04, 7.1362e+00, 1.5709e-01,
2DIAGNOSTIC,    24, -7.915043065291e-01, 1.230541419101e-04, 7.2492e+00, 1.1300e-01,
2DIAGNOSTIC,    25, -7.915115458574e-01, 6.767144050521e-05, 7.3594e+00, 1.1018e-01,
2DIAGNOSTIC,    26, -7.914958922878e-01, 3.483342636271e-05, 7.4514e+00, 9.1998e-02,
2DIAGNOSTIC,    27, -7.914751597285e-01, 2.431848065935e-05, 7.5442e+00, 9.2814e-02,
2DIAGNOSTIC,    28, -7.914779041205e-01, 1.558906467856e-05, 7.6533e+00, 1.0912e-01,
2DIAGNOSTIC,    29, -7.915069032947e-01, 8.884841404683e-06, 7.7964e+00, 1.4307e-01,
2DIAGNOSTIC,    30, -7.914837755525e-01, 5.563574204129e-06, 7.8883e+00, 9.1936e-02,
2DIAGNOSTIC,    31, -7.914846011998e-01, 5.084375618157e-06, 7.9827e+00, 9.4349e-02,
2DIAGNOSTIC,    32, -7.914868660413e-01, 5.069918010969e-06, 8.0776e+00, 9.4939e-02,
2DIAGNOSTIC,    33, -7.914917722049e-01, 5.036924335761e-06, 8.2269e+00, 1.4929e-01,
2DIAGNOSTIC,    34, -7.914919263466e-01, 5.040114412429e-06, 8.3196e+00, 9.2650e-02,
2DIAGNOSTIC,    35, -7.914927201547e-01, 4.942508897567e-06, 8.4125e+00, 9.2960e-02,
2DIAGNOSTIC,    36, -7.914944071362e-01, 4.498559931513e-06, 8.5051e+00, 9.2599e-02,
2DIAGNOSTIC,    37, -7.914968986287e-01, 3.893532323048e-06, 8.5984e+00, 9.3298e-02,
2DIAGNOSTIC,    38, -7.914990029754e-01, 3.139502150421e-06, 8.8090e+00, 2.1057e-01,
2DIAGNOSTIC,    39, -7.914990224018e-01, 2.331775294351e-06, 8.9358e+00, 1.2678e-01,
2DIAGNOSTIC,    40, -7.914990240224e-01, 1.417501008377e-06, 9.0807e+00, 1.4490e-01,
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC,     1, -5.214460596105e-01, 1.797693134862e+308, 1.0069e+01, 9.8787e-01,
2DIAGNOSTIC,     2, -5.223234371742e-01, 1.797693134862e+308, 1.0633e+01, 5.6447e-01,
2DIAGNOSTIC,     3, -5.235456616050e-01, 1.797693134862e+308, 1.1188e+01, 5.5535e-01,
2DIAGNOSTIC,     4, -5.253752416696e-01, 1.797693134862e+308, 1.1771e+01, 5.8294e-01,
2DIAGNOSTIC,     5, -5.282982714986e-01, 1.797693134862e+308, 1.2325e+01, 5.5403e-01,
2DIAGNOSTIC,     6, -5.314177760447e-01, 1.797693134862e+308, 1.2970e+01, 6.4440e-01,
2DIAGNOSTIC,     7, -5.324160104593e-01, 1.797693134862e+308, 1.3801e+01, 8.3127e-01,
2DIAGNOSTIC,     8, -5.326031253665e-01, 1.797693134862e+308, 1.4358e+01, 5.5662e-01,
2DIAGNOSTIC,     9, -5.330737088815e-01, 1.797693134862e+308, 1.5019e+01, 6.6122e-01,
2DIAGNOSTIC,    10, -5.333320544637e-01, 1.797693134862e+308, 1.5595e+01, 5.7648e-01,
2DIAGNOSTIC,    11, -5.334824565045e-01, 1.797693134862e+308, 1.6532e+01, 9.3670e-01,
2DIAGNOSTIC,    12, -5.335605938094e-01, 1.797693134862e+308, 1.7089e+01, 5.5659e-01,
2DIAGNOSTIC,    13, -5.337837929021e-01, 1.797693134862e+308, 1.7746e+01, 6.5703e-01,
2DIAGNOSTIC,    14, -5.339339863123e-01, 1.797693134862e+308, 1.8483e+01, 7.3743e-01,
2DIAGNOSTIC,    15, -5.340498778565e-01, 1.797693134862e+308, 1.9131e+01, 6.4837e-01,
2DIAGNOSTIC,    16, -5.342077343731e-01, 1.797693134862e+308, 1.9710e+01, 5.7829e-01,
2DIAGNOSTIC,    17, -5.344571831220e-01, 1.797693134862e+308, 2.0460e+01, 7.5049e-01,
2DIAGNOSTIC,    18, -5.344900474483e-01, 1.797693134862e+308, 2.1657e+01, 1.1967e+00,
2DIAGNOSTIC,    19, -5.344908918476e-01, 1.797693134862e+308, 2.2230e+01, 5.7335e-01,
2DIAGNOSTIC,    20, -5.344881838693e-01, 6.710113608043e-04, 2.2874e+01, 6.4361e-01,
2DIAGNOSTIC,    21, -5.344874581849e-01, 5.242427646021e-04, 2.3524e+01, 6.4959e-01,
2DIAGNOSTIC,    22, -5.344866875357e-01, 3.889184084705e-04, 2.4094e+01, 5.7079e-01,
2DIAGNOSTIC,    23, -5.344829004662e-01, 2.696236584970e-04, 2.4743e+01, 6.4824e-01,
2DIAGNOSTIC,    24, -5.344811722608e-01, 1.733393518074e-04, 2.5396e+01, 6.5358e-01,
2DIAGNOSTIC,    25, -5.344782594907e-01, 1.115979320199e-04, 2.6056e+01, 6.5953e-01,
2DIAGNOSTIC,    26, -5.344788114224e-01, 8.459865020741e-05, 2.6689e+01, 6.3362e-01,
2DIAGNOSTIC,    27, -5.344785039061e-01, 6.763016781419e-05, 2.7420e+01, 7.3067e-01,
2DIAGNOSTIC,    28, -5.344779277079e-01, 5.194192530716e-05, 2.8071e+01, 6.5119e-01,
2DIAGNOSTIC,    29, -5.344759761800e-01, 4.047737456967e-05, 2.8723e+01, 6.5223e-01,
2DIAGNOSTIC,    30, -5.344757761065e-01, 3.115576330763e-05, 2.9274e+01, 5.5108e-01,
2DIAGNOSTIC,    31, -5.344765621518e-01, 2.301348886666e-05, 2.9918e+01, 6.4394e-01,
2DIAGNOSTIC,    32, -5.344787153120e-01, 1.546584612162e-05, 3.0477e+01, 5.5890e-01,
2DIAGNOSTIC,    33, -5.344767258014e-01, 9.802157460617e-06, 3.1208e+01, 7.3077e-01,
2DIAGNOSTIC,    34, -5.344785916424e-01, 5.413381737179e-06, 3.2022e+01, 8.1360e-01,
2DIAGNOSTIC,    35, -5.344772529838e-01, 1.976595630577e-06, 3.2571e+01, 5.4958e-01,
Elapsed time (stage 1): 3.4011e+01

Stage 2
iterations = 50x20
convergence threshold = 1.0000e-06
convergence window size = 10
number of levels = 2
using the Mattes MI metric (number of bins = 56, weight = 1.0000e+00)
preprocessing:  winsorizing the image intensities
preprocessing:  histogram matching the images
Shrink factors (level 1 out of 2): [2, 2, 2]
Shrink factors (level 2 out of 2): [1, 1, 1]
smoothing sigmas per level: [1, 0]
regular sampling (percentage = 2.5000e-01)

*** Running SyN registration (varianceForUpdateField = 3.0000e+00, varianceForTotalField = 0.0000e+00) ***

XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
1DIAGNOSTIC,     1, -6.565429288236e-01, 1.797693134862e+308, 1.1599e+00, 1.1599e+00,
1DIAGNOSTIC,     2, -6.656679104864e-01, 1.797693134862e+308, 1.7232e+00, 5.6333e-01,
1DIAGNOSTIC,     3, -6.745637844515e-01, 1.797693134862e+308, 2.2882e+00, 5.6491e-01,
1DIAGNOSTIC,     4, -6.836074434093e-01, 1.797693134862e+308, 2.8372e+00, 5.4901e-01,
1DIAGNOSTIC,     5, -6.929479008265e-01, 1.797693134862e+308, 3.3716e+00, 5.3443e-01,
1DIAGNOSTIC,     6, -7.006759585328e-01, 1.797693134862e+308, 3.9204e+00, 5.4878e-01,
1DIAGNOSTIC,     7, -7.082377104246e-01, 1.797693134862e+308, 4.4545e+00, 5.3412e-01,
1DIAGNOSTIC,     8, -7.140589523568e-01, 1.797693134862e+308, 5.0035e+00, 5.4897e-01,
1DIAGNOSTIC,     9, -7.190772056663e-01, 1.797693134862e+308, 5.5388e+00, 5.3538e-01,
1DIAGNOSTIC,    10, -7.234786744401e-01, 6.312144716549e-03, 6.0745e+00, 5.3563e-01,
1DIAGNOSTIC,    11, -7.275418105474e-01, 5.213221242079e-03, 6.6113e+00, 5.3678e-01,
1DIAGNOSTIC,    12, -7.309304701969e-01, 4.255873426036e-03, 7.1453e+00, 5.3402e-01,
1DIAGNOSTIC,    13, -7.339067067687e-01, 3.433003769068e-03, 7.6827e+00, 5.3742e-01,
1DIAGNOSTIC,    14, -7.365370165511e-01, 2.752970399243e-03, 8.2179e+00, 5.3519e-01,
1DIAGNOSTIC,    15, -7.385481345634e-01, 2.217235286415e-03, 8.7587e+00, 5.4085e-01,
1DIAGNOSTIC,    16, -7.405350492599e-01, 1.788075554837e-03, 9.2921e+00, 5.3333e-01,
1DIAGNOSTIC,    17, -7.424005458919e-01, 1.466234805951e-03, 9.8288e+00, 5.3672e-01,
1DIAGNOSTIC,    18, -7.441075551083e-01, 1.211034872168e-03, 1.0367e+01, 5.3817e-01,
1DIAGNOSTIC,    19, -7.456380809139e-01, 1.007175847765e-03, 1.0904e+01, 5.3679e-01,
1DIAGNOSTIC,    20, -7.467396046420e-01, 8.388755218869e-04, 1.1440e+01, 5.3641e-01,
1DIAGNOSTIC,    21, -7.480223787661e-01, 7.090486468686e-04, 1.1976e+01, 5.3542e-01,
1DIAGNOSTIC,    22, -7.491735281374e-01, 6.057822974017e-04, 1.2513e+01, 5.3740e-01,
1DIAGNOSTIC,    23, -7.500892152796e-01, 5.209841982524e-04, 1.3061e+01, 5.4829e-01,
1DIAGNOSTIC,    24, -7.513201597122e-01, 4.575990808431e-04, 1.3599e+01, 5.3819e-01,
1DIAGNOSTIC,    25, -7.520944507358e-01, 3.997293859396e-04, 1.4151e+01, 5.5154e-01,
1DIAGNOSTIC,    26, -7.530804390430e-01, 3.533567297639e-04, 1.4686e+01, 5.3530e-01,
1DIAGNOSTIC,    27, -7.533649861855e-01, 3.079640147734e-04, 1.5261e+01, 5.7496e-01,
1DIAGNOSTIC,    28, -7.543738845994e-01, 2.746359234582e-04, 1.5821e+01, 5.5967e-01,
1DIAGNOSTIC,    29, -7.549188803731e-01, 2.453077646448e-04, 1.6380e+01, 5.5926e-01,
1DIAGNOSTIC,    30, -7.553247463300e-01, 2.140930229630e-04, 1.6931e+01, 5.5131e-01,
1DIAGNOSTIC,    31, -7.554101759186e-01, 1.817990256533e-04, 1.7481e+01, 5.5002e-01,
1DIAGNOSTIC,    32, -7.560408363248e-01, 1.560772405233e-04, 1.8032e+01, 5.5060e-01,
1DIAGNOSTIC,    33, -7.561143408445e-01, 1.283732700004e-04, 1.8586e+01, 5.5379e-01,
1DIAGNOSTIC,    34, -7.564734226859e-01, 1.082063780201e-04, 1.9134e+01, 5.4798e-01,
1DIAGNOSTIC,    35, -7.561642843073e-01, 8.394338313678e-05, 1.9682e+01, 5.4843e-01,
1DIAGNOSTIC,    36, -7.567690305224e-01, 7.047673199782e-05, 2.0231e+01, 5.4916e-01,
1DIAGNOSTIC,    37, -7.570094210641e-01, 5.612475260260e-05, 2.0784e+01, 5.5219e-01,
1DIAGNOSTIC,    38, -7.569889967842e-01, 4.709787308672e-05, 2.1338e+01, 5.5425e-01,
1DIAGNOSTIC,    39, -7.571615033388e-01, 4.126665743852e-05, 2.1890e+01, 5.5172e-01,
1DIAGNOSTIC,    40, -7.573087790646e-01, 3.722191411861e-05, 2.2439e+01, 5.4889e-01,
1DIAGNOSTIC,    41, -7.572034461355e-01, 2.942900328667e-05, 2.2988e+01, 5.4917e-01,
1DIAGNOSTIC,    42, -7.574550889358e-01, 2.731313879098e-05, 2.3538e+01, 5.5015e-01,
1DIAGNOSTIC,    43, -7.569107341268e-01, 1.837380043141e-05, 2.4101e+01, 5.6345e-01,
1DIAGNOSTIC,    44, -7.574541378420e-01, 1.630570774140e-05, 2.4665e+01, 5.6397e-01,
1DIAGNOSTIC,    45, -7.573744773165e-01, 9.149264252422e-06, 2.5227e+01, 5.6205e-01,
1DIAGNOSTIC,    46, -7.576590981541e-01, 8.854907337551e-06, 2.5790e+01, 5.6233e-01,
1DIAGNOSTIC,    47, -7.574550493585e-01, 8.056576045169e-06, 2.6355e+01, 5.6504e-01,
1DIAGNOSTIC,    48, -7.576667039784e-01, 8.135611332317e-06, 2.6920e+01, 5.6551e-01,
1DIAGNOSTIC,    49, -7.574962940677e-01, 7.361681448936e-06, 2.7488e+01, 5.6789e-01,
1DIAGNOSTIC,    50, -7.576362509116e-01, 8.125155033741e-06, 2.8062e+01, 5.7425e-01,
XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
1DIAGNOSTIC,     1, -5.810468766265e-01, 1.797693134862e+308, 3.2743e+01, 4.6806e+00,
1DIAGNOSTIC,     2, -5.823095816360e-01, 1.797693134862e+308, 3.6472e+01, 3.7288e+00,
1DIAGNOSTIC,     3, -5.833609407673e-01, 1.797693134862e+308, 4.0127e+01, 3.6555e+00,
Standard error:
Killed
Return code: 137
Interface Registration failed to run. .
2017-09-18 17:45:31,030 workflow:ERROR ['Node SpatialNormalization.a1 failed to run on host 8bb44527869c.']
2017-09-18 17:46:46,291 niworkflows:INFO Successful spatial normalization (retry #0).
2017-09-18 17:46:46,303 niworkflows:INFO Report - setting fixed (/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/fixed_masked.nii.gz) and moving (/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2017-09-18 17:46:46,305 niworkflows:INFO Generating visual report
2017-09-18 17:47:04,801 niworkflows:INFO Successfully created report (/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/SpatialNormalization/report.svg)
2017-09-18 17:48:10,940 workflow:ERROR could not run node: workflow_enumerator.anatMRIQCT1w.segmentation.a0
2017-09-18 17:48:10,941 workflow:ERROR could not run node: workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization.a1
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/mriqc", line 11, in <module>
    load_entry_point('mriqc==0.9.8.post1', 'console_scripts', 'mriqc')()
  File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py", line 325, in main
    workflow.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 590, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 279, in run
    report_nodes_not_run(notrun)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 101, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for 

And this is one of the the crash logs:

Node: workflow_enumerator.anatMRIQCT1w.segmentation
Working directory: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/segmentation

Node inputs:

args = <undefined>
bias_iters = <undefined>
bias_lowpass = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
hyper = <undefined>
ignore_exception = False
img_type = 1
in_files = ['/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/sstrip_orig_vol/sub-CF1036ENT_T1w_conformed_calc.nii.gz']
init_seg_smooth = <undefined>
init_transform = <undefined>
iters_afterbias = <undefined>
manual_seg = <undefined>
mixel_smooth = <undefined>
no_bias = <undefined>
no_pve = <undefined>
number_classes = <undefined>
other_priors = <undefined>
out_basename = segment
output_biascorrected = <undefined>
output_biasfield = <undefined>
output_type = NIFTI_GZ
probability_maps = <undefined>
segment_iters = <undefined>
segments = True
terminal_output = stream
use_priors = <undefined>
verbose = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 52, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 372, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 613, in _run_command
    result = self._interface.run()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1083, in run
    runtime = self._run_wrapper(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1757, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1791, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1715, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
fast -t 1 -o segment -g -S 1 /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-CF1036ENT..anat..sub-CF1036ENT_T1w.nii/segmentation/sub-CF1036ENT_T1w_conformed_calc.nii.gz
Standard output:

Standard error:
Killed

Return code: 137
Interface FAST failed to run.

How can I fix this issue?

Thanks!!

oesteban commented 6 years ago

This looks like you are hitting the default memory limitations of docker in Mac: https://github.com/poldracklab/mriqc/issues/388#issuecomment-281208441

Please check this section of the documentation (http://mriqc.readthedocs.io/en/stable/docker.html) and let us know if that fixed the issue.

oesteban commented 6 years ago

Hi @vnckppl, any updates on this problem?

I think this is a problem of hitting the memory maximum, unrelated to #536. I'll close it for now, please reopen if revising memory limits did not work.

vnckppl commented 6 years ago

Dear sir/madam,

Yes, increasing the memory size fixed the problem for me.

Thank you,

Best,

Vincent

On Nov 9, 2017, at 12:59 AM, Oscar Esteban notifications@github.com<mailto:notifications@github.com> wrote:

Hi @vnckpplhttps://github.com/vnckppl, any updates on this problem?

I think this is a problem of hitting the memory maximum, unrelated to #536https://github.com/poldracklab/mriqc/issues/536. I'll close it for now, please reopen if revising memory limits did not work.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/poldracklab/mriqc/issues/644#issuecomment-343273881, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AOah-pEZVvH0Gi22_L_NvRNOobCHN0Cjks5s01mggaJpZM4PbUFV.