Package: ants
Version: 1.9+svn532-3
Severity: normal
P.S. CCing all possibly interested parties ;)
According to docstring of WarpTimeSeriesImageMultiTransform sequence of
necessary transformations could be arbitrarily long. Having applied
a sequence
MNI -> inverse warp -> inverse affine -> inverse affine
produces different (and looks like incorrect) result from if I do
transformations in two steps, e.g.
MNI -> inverse warp -> inverse affine
and then result of previous given for the final inverse affine.
Here is output of running reproduce.sh. All data, script and
results are available from
http://www.onerussian.com/Linux/bugs/ants.2steps/
I investigate the result by comparing mni2bold.nii.gz and mni2bold-2.nii.gz
overlayed on top of epi_template.nii.gz. mni2bold.nii.gz seems to be offset
toward anterior
$> ./reproduce.sh
I: Lets do directly all the steps at once
Running: WarpTimeSeriesImageMultiTransform 4 mni.nii.gz
mni2bold.nii.gz -R epi_template.nii.gz anat2mni_InverseWarp.nii.gz
-i anat2mni_Affine.txt -i raiders_func2anat_Affine.txt --use-NN
FIELD: anat2mni_InverseWarp.nii.gz
AFFINE-INV: anat2mni_Affine.txt
AFFINE-INV: raiders_func2anat_Affine.txt
moving_image_filename: mni.nii.gz
output_image_filename: mni2bold.nii.gz
reference_image_filename: epi_template.nii.gz
[0/3]: FIELD: anat2mni_InverseWarp.nii.gz
[1/3]: AFFINE-INV: anat2mni_Affine.txt
[2/3]: AFFINE-INV: raiders_func2anat_Affine.txt
Four-D image size: [182, 218, 182, 1]
4D-In-Spc [1, 1, 1, 1]
4D-In-Org [-90, 126, -72, 0]
4D-In-Size [182, 218, 182, 1]
4D-In-Dir 1 0 0 0
0 -1 0 0
0 0 1 0
0 0 0 1
......
4D-Out-Spc [3, 3, 3, 1]
4D-Out-Org [-70.5, -75.759, 93.1085, 0]
4D-Out-Size [64, 64, 48, 1]
4D-Out-Dir -0 0 1 0
1 -0 0 0
0 -1 -0 0
0 0 0 1
Use Nearest Neighbor interpolation
0 % done ... -0 0 1
1 -0 0
0 -1 -0
100 % complete
I: Lets do directly all the steps at once
Step 1 mni->anat: WarpTimeSeriesImageMultiTransform 4 mni.nii.gz
mni2anat.nii.gz -R brain_avg.nii.gz anat2mni_InverseWarp.nii.gz -i
anat2mni_Affine.txt --use-NN
FIELD: anat2mni_InverseWarp.nii.gz
AFFINE-INV: anat2mni_Affine.txt
moving_image_filename: mni.nii.gz
output_image_filename: mni2anat.nii.gz
reference_image_filename: brain_avg.nii.gz
[0/2]: FIELD: anat2mni_InverseWarp.nii.gz
[1/2]: AFFINE-INV: anat2mni_Affine.txt
Four-D image size: [182, 218, 182, 1]
4D-In-Spc [1, 1, 1, 1]
4D-In-Org [-90, 126, -72, 0]
4D-In-Size [182, 218, 182, 1]
4D-In-Dir 1 0 0 0
0 -1 0 0
0 0 1 0
0 0 0 1
......
4D-Out-Spc [1, 1, 1, 1]
4D-Out-Org [-86.8253, -128, 132.723, 0]
4D-Out-Size [256, 256, 176, 1]
4D-Out-Dir -0 0 1 0
1 -0 0 0
0 -1 -0 0
0 0 0 1
Use Nearest Neighbor interpolation
0 % done ... -0 0 1
1 -0 0
0 -1 -0
100 % complete
Step 2 anat->mni: WarpTimeSeriesImageMultiTransform 4
mni2anat.nii.gz mni2bold-2.nii.gz -R epi_template.nii.gz -i
raiders_func2anat_Affine.txt --use-NN
AFFINE-INV: raiders_func2anat_Affine.txt
moving_image_filename: mni2anat.nii.gz
output_image_filename: mni2bold-2.nii.gz
reference_image_filename: epi_template.nii.gz
[0/1]: AFFINE-INV: raiders_func2anat_Affine.txt
Four-D image size: [256, 256, 176, 1]
4D-In-Spc [1, 1, 1, 1]
4D-In-Org [-86.8253, -128, 132.723, 0]
4D-In-Size [256, 256, 176, 1]
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, 1]
4D-Out-Org [-70.5, -75.759, 93.1085, 0]
4D-Out-Size [64, 64, 48, 1]
4D-Out-Dir -0 0 1 0
1 -0 0 0
0 -1 -0 0
0 0 0 1
-- System Information:
Debian Release: squeeze/sid
APT prefers unstable
APT policy: (901, 'unstable'), (900, 'testing'), (300, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages ants depends on:
ii libc6 2.11.2-2 Embedded GNU C Library:
Shared lib
ii libgcc1 1:4.4.4-6 GCC support library
ii libinsighttoolkit3.18 3.18.0-3+b1 Image processing
toolkit for regis
ii libstdc++6 4.4.4-6 The GNU Standard C++ Library v3
ants recommends no packages.
Versions of packages ants suggests:
ii fsl 4.1.6-1 analysis tools for
FMRI, MRI and D
pn gridengine-client <none> (no description available)
-- no debconf information
--
.-.
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Linux User ^^-^^ [175555]
