Comments (17)
stnava
commented on August 25, 2024
sounds more like an ANTs issue - but either way we need to know more about
your platform, compiler, etc.
brian
On Tue, Mar 10, 2015 at 10:47 AM, Stefan Schlager [email protected]
wrote:
I installed the latest ANTsR version from github and noticed that
selecting any affine transform causes a segfault. I checked using the
command line tool built in src/antb against an older version from
2014-09-29 that works:
old version (runs fine):~/GIT/DEV/ANTSbuild/bin/antsRegistration -d 3 -m mattes[skull1.mha,skull2.mha,1,32,Regular,0.1] -t rigid[ 1.0 ] -c [1000x100x10,1e-8,20] -s 4x2x1vox -f 3x2x1 -u 1 -o [skull1.mha_fixed_skull1.mha_moving_custom,skull1.mha_fixed_skull1.mha_moving_custom_diff.nii.gz,skull1.mha_fixed_skull1.mha_moving_custom_inv.nii.gz]
new version:
~/GIT/DEV/ANTsR/src/antb/bin/antsRegistration -d 3 -m mattes[skull1.mha,skull2.mha,1,32,Regular,0.1] -t rigid[ 1.0 ] -c [1000x100x10,1e-8,20] -s 4x2x1vox -f 3x2x1 -u 1 -o [skull1.mha_fixed_skull1.mha_moving_custom,skull1.mha_fixed_skull1.mha_moving_custom_diff.nii.gz,skull1.mha_fixed_skull1.mha_moving_custom_inv.nii.gz]
fails with
All_Command_lines_OK
Using double precision for computations.
number of levels = 3
fixed image: skull1.mha
moving image: skull2.mha
Dimension = 3
Number of stages = 1
Use Histogram Matching true
Winsorize image intensities false
Lower quantile = 0
Upper quantile = 1
Stage 1 State
Image metric = Mattes
Fixed image = Image (0x3c44700)
RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 639
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: 448
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
Spacing: [1.5, 1.5, 1.5]
Origin: [-88.5114, -114.68, -157.958]
Direction:
1 0 0
0 1 0
0 0 1IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667Inverse Direction:
1 0 0
0 1 0
0 0 1PixelContainer:
ImportImageContainer (0x3c449c0)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 445
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f131f95b010
Container manages memory: true
Size: 3122730
Capacity: 3122730Moving image = Image (0x3c48710)RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 640
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: 637
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
Spacing: [1.5, 1.5, 1.5]
Origin: [-85.1487, -103.461, -145.826]
Direction:
1 0 0
0 1 0
0 0 1IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667Inverse Direction:
1 0 0
0 1 0
0 0 1PixelContainer:
ImportImageContainer (0x3c49c30)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 634
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f131e42d010
Container manages memory: true
Size: 2775740
Capacity: 2775740Weighting = 1 Sampling strategy = regular Number of bins = 32 Radius = 4 Sampling percentage = 0.1Transform = Rigid
Gradient step = 1
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
Registration using 1 total stages.Stage 0
iterations = 1000x100x10
convergence threshold = 1e-08
convergence window size = 20
number of levels = 3
using the Mattes MI metric (number of bins = 32, weight = 1)
preprocessing: histogram matching the images
Shrink factors (level 1 out of 3): [3, 3, 3]
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, 1]
regular sampling (percentage = 0.1)
Segmentation fault (core dumped)Am I missing something?
Best
Stefan—
Reply to this email directly or view it on GitHub
#17.
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zarquon42b
commented on August 25, 2024
Hi Brian
sorry, for my negligance.
Ubuntu 14.04 64 bit
gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
What else do you need?
The thing was, that I realized that my old code (from last October) did not run anymore after installing a new version of ANTsR. As I still had an old version of ANTs but not ANTsR, I tried to compare the results when using the same arguments with the command line. I
BTW: SyN registration without preceding affine registrations works fine.
Best
Stefan
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ntustison
commented on August 25, 2024
Can you share those images? I'm not able to reproduce the error with my own test images.
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stnava
commented on August 25, 2024
ok - will look into it - first pass adding a test call to travis ants
brian
On Tue, Mar 10, 2015 at 12:28 PM, Stefan Schlager [email protected]
wrote:
Hi Brian
sorry, for my negligance.Ubuntu 14.04 64 bit
gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)What else do you need?
The thing was, that I realized that my old code (from last October) did
not run anymore after installing a new version of ANTsR. As I still had an
old version of ANTs but not ANTsR, I tried to compare the results when
using the same arguments with the command line. I
BTW: SyN registration without preceding affine registrations works fine.Best
Stefan—
Reply to this email directly or view it on GitHub
#17 (comment).
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stnava
commented on August 25, 2024
@ntustison may be right in that the issue may be specific to these images ... travis testing looks ok: https://s3.amazonaws.com/archive.travis-ci.org/jobs/53831111/log.txt
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zarquon42b
commented on August 25, 2024
I will run more tests tomorrow, and if I don't find any errors on my parts, I will provide sample data and scripts.
Best
Stefan
from antsr.
zarquon42b
commented on August 25, 2024
Is there a way, I can send you the data privately?
from antsr.
stnava
commented on August 25, 2024
depends on how you define "privately" (recalling snowden etc) but
wetransfer.com lets you send data to select individuals and the data link
is only active for a week or so
brian
On Tue, Mar 10, 2015 at 2:35 PM, Stefan Schlager [email protected]
wrote:
Is there a way, I can send you the data privately?
—
Reply to this email directly or view it on GitHub
#17 (comment).
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zarquon42b
commented on August 25, 2024
I already sent an email to the addresses (yours and ntustison's) in your commit logs.
Best
Stefan
from antsr.
ntustison
commented on August 25, 2024
Hmmm, for some reason it's seg faulting without a transform initialization. Try adding this to see if it works on your end
-r [ skull1.mha , skull2.mha , 1]
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stnava
commented on August 25, 2024
ahh - yes ... that would do it ... i've noticed the same thing recently.
brian
On Tue, Mar 10, 2015 at 3:44 PM, Nick Tustison [email protected]
wrote:
Hmmm, for some reason it's seg faulting without a transform
initialization. Try adding this to see if it works on your end-r [ skull1.mha , skull2.mha , 1]
—
Reply to this email directly or view it on GitHub
#17 (comment).
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zarquon42b
commented on August 25, 2024
Hi this
gives no segfault but
All_Command_lines_OK
Using double precision for computations.
=============================================================================
The composite transform comprises the following transforms (in order):
1. Center of mass alignment using fixed image: skull1.mha and moving image: skull2.mha (type = Euler3DTransform)
=============================================================================
number of levels = 3
fixed image: skull1.mha
moving image: skull2.mha
Dimension = 3
Number of stages = 1
Use Histogram Matching true
Winsorize image intensities false
Lower quantile = 0
Upper quantile = 1
Stage 1 State
Image metric = Mattes
Fixed image = Image (0x44a68d0)
RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1683
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: 1492
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
Spacing: [1.5, 1.5, 1.5]
Origin: [-88.5114, -114.68, -157.958]
Direction:
1 0 0
0 1 0
0 0 1
IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5
PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667
Inverse Direction:
1 0 0
0 1 0
0 0 1
PixelContainer:
ImportImageContainer (0x44ba230)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1489
Debug: Off
Object Name:
Observers:
none
Pointer: 0x45fd080
Container manages memory: true
Size: 3122730
Capacity: 3122730
Moving image = Image (0x44c1e00)
RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1684
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: 1681
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
Spacing: [1.5, 1.5, 1.5]
Origin: [-85.1487, -103.461, -145.826]
Direction:
1 0 0
0 1 0
0 0 1
IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5
PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667
Inverse Direction:
1 0 0
0 1 0
0 0 1
PixelContainer:
ImportImageContainer (0x44af720)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1678
Debug: Off
Object Name:
Observers:
none
Pointer: 0x5dd8310
Container manages memory: true
Size: 2775740
Capacity: 2775740
Weighting = 1
Sampling strategy = regular
Number of bins = 32
Radius = 4
Sampling percentage = 0.1
Transform = Rigid
Gradient step = 1
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
Registration using 1 total stages.
Stage 0
iterations = 1000x100x10
convergence threshold = 1e-08
convergence window size = 20
number of levels = 3
using the Mattes MI metric (number of bins = 32, weight = 1)
preprocessing: histogram matching the images
Shrink factors (level 1 out of 3): [3, 3, 3]
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, 1]
regular sampling (percentage = 0.1)
*** Running Euler3DTransform registration ***
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC, 1, -3.720398661092e-01, 1.797693134862e+308, 7.0343e-01, 7.0343e-01,
.
.
.
2DIAGNOSTIC, 9, -1.522124430969e-01, 1.797693134862e+308, 7.5271e+00, 3.0540e-01,
2DIAGNOSTIC, 10, -1.523563157790e-01, 1.797693134862e+308, 7.8510e+00, 3.2386e-01,
Elapsed time (stage 0): 7.9909e+00
Total elapsed time: 7.9939e+00
But the rigid transform is skipped.
If I combine multiple non-elastic transformations it runs the Euler3DTransform multiple times.
But: I arbitrarily checked out an earlier version of ANTS in ANTsR/src/ANTS/ANTS-build :
(commit 002cc39f524c52f5970fbdd74dac4bc5f7035a09
Author: stnava <[email protected]>
Date: Mon Jan 5 13:12:27 2015 -0600
and recompiled (using R CMD INSTALL), now everything works again. First runnint the Euler3D and then the rigid transformation.
from antsr.
stnava
commented on August 25, 2024
yes - i've also noticed this ... not sure if it's the reporting that's
wrong or if it's the actual transformation. do you happen to know?
brian
On Tue, Mar 10, 2015 at 4:18 PM, Stefan Schlager [email protected]
wrote:
Hi this
gives no segfault butAll_Command_lines_OK
Using double precision for computations.
The composite transform comprises the following transforms (in order):
1. Center of mass alignment using fixed image: skull1.mha and moving image: skull2.mha (type = Euler3DTransform)
number of levels = 3
fixed image: skull1.mha
moving image: skull2.mha
Dimension = 3
Number of stages = 1
Use Histogram Matching true
Winsorize image intensities false
Lower quantile = 0
Upper quantile = 1
Stage 1 State
Image metric = Mattes
Fixed image = Image (0x44a68d0)
RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1683
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: 1492
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [117, 157, 170]
Spacing: [1.5, 1.5, 1.5]
Origin: [-88.5114, -114.68, -157.958]
Direction:
1 0 0
0 1 0
0 0 1IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667Inverse Direction:
1 0 0
0 1 0
0 0 1PixelContainer:
ImportImageContainer (0x44ba230)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1489
Debug: Off
Object Name:
Observers:
none
Pointer: 0x45fd080
Container manages memory: true
Size: 3122730
Capacity: 3122730Moving image = Image (0x44c1e00)RTTI typeinfo: itk::Image<double, 3u>
Reference Count: 2
Modified Time: 1684
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: 1681
RealTimeStamp: 0 seconds
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [121, 148, 155]
Spacing: [1.5, 1.5, 1.5]
Origin: [-85.1487, -103.461, -145.826]
Direction:
1 0 0
0 1 0
0 0 1IndexToPointMatrix:
1.5 0 0
0 1.5 0
0 0 1.5PointToIndexMatrix:
0.666667 0 0
0 0.666667 0
0 0 0.666667Inverse Direction:
1 0 0
0 1 0
0 0 1PixelContainer:
ImportImageContainer (0x44af720)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1678
Debug: Off
Object Name:
Observers:
none
Pointer: 0x5dd8310
Container manages memory: true
Size: 2775740
Capacity: 2775740Weighting = 1 Sampling strategy = regular Number of bins = 32 Radius = 4 Sampling percentage = 0.1Transform = Rigid
Gradient step = 1
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
Registration using 1 total stages.Stage 0
iterations = 1000x100x10
convergence threshold = 1e-08
convergence window size = 20
number of levels = 3
using the Mattes MI metric (number of bins = 32, weight = 1)
preprocessing: histogram matching the images
Shrink factors (level 1 out of 3): [3, 3, 3]
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, 1]
regular sampling (percentage = 0.1)*** Running Euler3DTransform registration ***
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
2DIAGNOSTIC, 1, -3.720398661092e-01, 1.797693134862e+308, 7.0343e-01, 7.0343e-01,
.
.
.
2DIAGNOSTIC, 9, -1.522124430969e-01, 1.797693134862e+308, 7.5271e+00, 3.0540e-01,
2DIAGNOSTIC, 10, -1.523563157790e-01, 1.797693134862e+308, 7.8510e+00, 3.2386e-01,
Elapsed time (stage 0): 7.9909e+00Total elapsed time: 7.9939e+00
But the rigid transform is skipped.
If I combine multiple non-elastic transformations it runs the
Euler3DTransform multiple times.But: I arbitrarily checked out an earlier version of ANTS in
ANTsR/src/ANTS/ANTS-build :(commit 002cc39f524c52f5970fbdd74dac4bc5f7035a09
Author: stnava [email protected]
Date: Mon Jan 5 13:12:27 2015 -0600and recompiled (using R CMD INSTALL), now everything works again. First
runnint the Euler3D and then the rigid transformation.—
Reply to this email directly or view it on GitHub
#17 (comment).
from antsr.
ntustison
commented on August 25, 2024
The Euler3DTransform is the rigid transform being employed, i.e. it's not being skipped. This was part of the code clean-up I performed a little bit ago. I'll figure out why it's seg-faulting but, for now, just be sure to use the initialization.
from antsr.
ntustison
commented on August 25, 2024
Okay, this is fixed in ANTs. Brian, can we update ANTsR with this or do we wait?
from antsr.
stnava
commented on August 25, 2024
Yes. All one needs to do is change antstag in configure.
On Mar 10, 2015 9:07 PM, "Nick Tustison" [email protected] wrote:
Okay, this is fixed in ANTs. Brian, can we update ANTsR with this or do we
wait?—
Reply to this email directly or view it on GitHub
#17 (comment).
from antsr.
ntustison
commented on August 25, 2024
Okay, done.
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