Your message dated Sat, 31 Jul 2010 20:50:27 +0000
with message-id <[email protected]>
and subject line Bug#587200: fixed in insighttoolkit 3.18.0-4
has caused the Debian Bug report #587200,
regarding itk::NiftiImageIO::Read: sever memory leak (patch provided)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
587200: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=587200
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: ants
Version: 1.9+svn532-2
Severity: normal
I tried warping a timeseries image with a warpfield and two consecutive
affine transformations, but it fails because the process requires a huge
amount of memory, probably due to a leak. This is the timeseries images:
m...@head1 /tmp % fslinfo bold.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 48
dim4 1101
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 3.0000000000
pixdim4 3.0000000000
cal_max 1462.2584
cal_min 0.0000
file_type NIFTI-1+
and here the reference image:
m...@head1 /tmp % fslinfo MNI.nii.gz
data_type INT16
dim1 64
dim2 73
dim3 64
dim4 1
datatype 4
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
I tried to run something like this:
WarpTimeSeriesImageMultiTransform 4 bold.nii.gz warped4.nii.gz -R MNI.nii.gz
myWarp.nii.gz myAffine.txt otherAffine.txt
The process seems to run fine (usual output). However, after about 20%
completion (about 20min time) it already consumes more than 20GB and
that consumption grows steadily. I assume it processes the image volume
by volume and there is a memory leak somewhere. The process eventually
dies when it exceeds the machines memory (64GB!).
I tried to trim the problem down to be able to debug it and made an
image with only the first two volumes of bold.nii.gz. However, running
the above command with this image points to another problem:
m...@head1 /tmp % WarpTimeSeriesImageMultiTransform 4 example4d.nii.gz
warped4d.nii.gz -R MNI.nii.gz myWarp.nii.gz myAffine.txt otherAffine.txt
FIELD: myWarp.nii.gz
AFFINE: myAffine.txt
AFFINE: otherAffine.txt
moving_image_filename: example4d.nii.gz
output_image_filename: warped4d.nii.gz
reference_image_filename: MNI.nii.gz
[0/3]: FIELD: myWarp.nii.gz
[1/3]: AFFINE: myAffine.txt
[2/3]: AFFINE: otherAffine.txt
Four-D image size: [64, 64, 48, 2]
4D-In-Spc [3, 3, 3, 3]
4D-In-Org [-66.1627, -88.7711, 84.4337, 0]
4D-In-Size [64, 64, 48, 2]
4D-In-Dir -0 0 1 0
1 -0 0 0
0 -1 -0 0
0 0 0 1
......
4D-Out-Spc [3, 3, 3, 3]
4D-Out-Org [-90, 126, -72, 0]
4D-Out-Size [64, 73, 64, 2]
4D-Out-Dir 1 0 0 0
0 -1 0 0
0 0 1 0
0 0 0 1
E: Child terminated by signal ‘Floating point exception’
(+ core dump)
Finally, to see whether there is a problem with the volumes, the
warpfield or the affines I ran this command on an image with only the
first volume of bold.nii.gz:
WarpImageMultiTransform 3 example3d.nii.gz warped3d.nii.gz -R MNI.nii.gz
myWarp.nii.gz myAffine.txt otherAffine.txt
and it behaves exactly like it should and yields the results I wanted to
see. So I guess the transformations and input images are fine and the
problem lies somewhere in WarpTimeSeriesImageMultiTransform.
Thanks in advance,
Michael
--- End Message ---
--- Begin Message ---
Source: insighttoolkit
Source-Version: 3.18.0-4
We believe that the bug you reported is fixed in the latest version of
insighttoolkit, which is due to be installed in the Debian FTP archive:
insighttoolkit3-examples_3.18.0-4_all.deb
to main/i/insighttoolkit/insighttoolkit3-examples_3.18.0-4_all.deb
insighttoolkit_3.18.0-4.diff.gz
to main/i/insighttoolkit/insighttoolkit_3.18.0-4.diff.gz
insighttoolkit_3.18.0-4.dsc
to main/i/insighttoolkit/insighttoolkit_3.18.0-4.dsc
libinsighttoolkit3-dev_3.18.0-4_amd64.deb
to main/i/insighttoolkit/libinsighttoolkit3-dev_3.18.0-4_amd64.deb
libinsighttoolkit3-java_3.18.0-4_all.deb
to main/i/insighttoolkit/libinsighttoolkit3-java_3.18.0-4_all.deb
libinsighttoolkit3-jni_3.18.0-4_amd64.deb
to main/i/insighttoolkit/libinsighttoolkit3-jni_3.18.0-4_amd64.deb
libinsighttoolkit3.18_3.18.0-4_amd64.deb
to main/i/insighttoolkit/libinsighttoolkit3.18_3.18.0-4_amd64.deb
python-insighttoolkit3_3.18.0-4_amd64.deb
to main/i/insighttoolkit/python-insighttoolkit3_3.18.0-4_amd64.deb
tcl8.5-insighttoolkit3_3.18.0-4_amd64.deb
to main/i/insighttoolkit/tcl8.5-insighttoolkit3_3.18.0-4_amd64.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Steve M. Robbins <[email protected]> (supplier of updated insighttoolkit package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Fri, 30 Jul 2010 23:42:36 -0500
Source: insighttoolkit
Binary: libinsighttoolkit3.18 libinsighttoolkit3-java libinsighttoolkit3-jni
python-insighttoolkit3 tcl8.5-insighttoolkit3 libinsighttoolkit3-dev
insighttoolkit3-examples
Architecture: source all amd64
Version: 3.18.0-4
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Steve M. Robbins <[email protected]>
Description:
insighttoolkit3-examples - Image processing toolkit for registration and
segmentation - exam
libinsighttoolkit3-dev - Image processing toolkit for registration and
segmentation - deve
libinsighttoolkit3-java - Image processing toolkit for registration and
segmentation - Java
libinsighttoolkit3-jni - Image processing toolkit for registration and
segmentation - JNI
libinsighttoolkit3.18 - Image processing toolkit for registration and
segmentation - runt
python-insighttoolkit3 - Image processing toolkit for registration and
segmentation - Pyth
tcl8.5-insighttoolkit3 - Image processing toolkit for registration and
segmentation - Tcl
Closes: 586928 587200
Changes:
insighttoolkit (3.18.0-4) unstable; urgency=low
.
* rules: Use cmake.mk instead of makefile.mk; drop common-configure-arch
rule.
.
* CMakeCache.txt.debian: Remove.
* rules: Move contents of CMakeCache.txt.debian into rules as "-D"
options to cmake.
.
* patches/nifti-memleak.patch: New. Fix memory leak in itkNiftiImageIO.
Closes: #587200.
.
* rules: install InsightValgrind.supp and InsightVxlValgrind.supp.
Closes: #586928.
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--- End Message ---
