Doug,
Sorry if I muddied things by going into the significant digits - accurate to 5 seems reasonable. I was simply meaning to say that the rotation and scaling parameters are not the issue, to save the reader time inspecting them.
The translations (final three parameters) are off by anywhere 3 to 54mm, though.
LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766
I'm guessing lta_convert has the wrong model of the origin in ITK style affines, at least as applied by antsApplyTransforms.
Chris
________________________________________
From:
freesurfer-bounces@nmr.mgh.harvard.edu <
freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <
greve@nmr.mgh.harvard.edu>
Sent: Monday, October 16, 2017 12:39:28 PM
To:
freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms
Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.
On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
Hi,
I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
The following produces a well-aligned output:
mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
As does the following:
lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt
However, if one skips the FSL step, the registration is quite far off:
lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt
Comparing the ITK transform files:
LTA-FSL-ITK
#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 -0.01079971161879626 0.872329255299452 -0.42602926756857834 -0.004755964529051335 0.42420535065804454 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
FixedParameters: 0 0 0
LTA-ITK
#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.98950976133346558 0.011126830242574215 -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
FixedParameters: 0 0 0
To 5 significant digits, these are the same, except the last three (translation) parameters. And the `AffineTransform_double_3_3` is different from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this has any effect.
Here is the original LTA:
type = 1 # LINEAR_RAS_TO_RAS
nxforms = 1
mean = 0.0000 0.0000 0.0000
sigma = 1.0000
1 4 4
1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 -2.332115173339844e+00
1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 2.507942199707031e+00
4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 -1.201664733886719e+01
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999998807907104e-01
src volume info
valid = 1 # volume info valid
filename = /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
volume = 64 64 34
voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
cras = -1.090248107910156e+00 -1.071614074707031e+01 1.619928741455078e+01
dst volume info
valid = 1 # volume info valid
filename = /scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz
volume = 160 192 192
voxelsize = 1.000000000000000e+00 1.333333015441895e+00 1.333333015441895e+00
xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
cras = -3.000000000000000e+00 2.999969482421875e+00 -8.000030517578125e+00
subject sub-02
fscale 0.100000
If it would be useful, I can provide any relevant images for testing.
--
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer