Hi Chris, thanks, can you send the images and the exact commands. We have had success in the past, could be that you have a special case (e.g. maybe we never tested registration across different resolutions or whatever?).
Thanks, Martin https://gate.nmr.mgh.harvard.edu/filedrop2/ <https://gate.nmr.mgh.harvard.edu/filedrop2/> > On 16. Oct 2017, at 19:37, Christopher Markiewicz <markiew...@stanford.edu> > wrote: > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Monday, October 16, 2017 12:39:28 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: 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.edu > https://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. 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