External Email - Use Caution Hi Yazdan,
Thanks for the information. Is the “PSR/LAS/RAS Orientation of image” you mentioned the same ‘Orientation’ reported by mri_info? I believe the Orientation reported by mri_info tells the data ordering on disk. It is not the anatomical space. Both nii and mgz are RAS. I tried the method described in this posting (https://secure-web.cisco.com/1APqgiyEgb8KoTku5P1376REqaOm8LWn2j_60Z3VrODJu7DE6KX_dDgXHnyeNktNrvoY9UE8pztcC7TCnb9h1PgIAXAP6kEd4Gd_C0ixAxfgnBJlou_FkCewSW8_ccaXgIndWa-TX4_0jh53UNXJJWnohUqlbf2uexaNApI9yRCI9Gc05xXT4w5kh-xBOJ6yQ0TBjjMzxGKeQojzPYME53MhQwIt2Rq_rcHXbAkV3NMfjxZvvtrICQCv6QrXBdAX9xMR0IqW0uqjjVP1vDsXuQQ/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F71441883%2Fhow-to-get-transformation-affine-from-itk-registration) registration_ras = flip_LPS_RAS @ registration_lps @ flip_LPS_RAS registration_lps is ants.txt read in by lta_convert. I converted inv(registration_ras) to vox2vox using the vox2ras printed by mri_info. I got the same results as lta_convert. I’m wondering if there are other ways to verify ants_0GenericAffine.mat and ants.txt generated by Ants. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yazdan Rezaee Jouryabi Sent: Sunday, October 8, 2023 10:04 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix External Email - Use Caution Hi Yujing, Sure. the results of applying mri_info are attached below Bests, Yazdan. On Fri, 6 Oct 2023 at 23:19, Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote: External Email - Use Caution Hi Yazdan, Thank you for the detailed explanation. I’m wondering if you could send output of mri_info for Image.nii, fsl_resampled.nii.gz, fslregistered.nii.gz, freesurfer.nii, and output from ANTs. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Yazdan Rezaee Jouryabi Sent: Friday, September 29, 2023 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix External Email - Use Caution Hi Yujing, I'll try to explain it more explicitly, I rerun my Code and show the results beyond attaching the Registration files too. Consider a 3D-Nifti image called "Image.nii" the steps bellow executed in order: 0- Every time we Will generate a random Registration Matrix and Save it under the name "fsl.mat" which is the desired Registration matrix. ============================================================================== fsl.mat := [[ 0.95509431, -0.28438761, 0.08317783, -5. ] [ 0.2961434, 0.90701597, -0.29936787, -5. ] [ 0.00969289, 0.31055712, 0.9505053, -2. ] [ 0., 0., 0., 1. ]] ============================================================================== 1- using a known registration matrice (called and attached in the first message and this message as "fsl.mat") resample the "Image.nii" to second Image called "fsl_resampled.nii" Command : flirt -ref ./Image.nii -in ./Image.nii -applyxfm -init ./fsl.mat -out ./fsl_resampled.nii -interp spline 2- find out the registration matrices using Registration Methods, here we will use FSL, FreesSurefer, ANTs: 2.1. FSL Commands: =============================================================================== Command : flirt -in ./Image.nii -out ./fslregistered.nii.gz -ref ./fsl_resampled.nii.gz -cost normmi -dof 6 -omat ./fslregistered.mat -interp spline =============================================================================== fslregistered : 0.9551458402 -0.2842262621 0.08313877187 -5.029802253 0.2959789517 0.9070999982 -0.2992758021 -5.014360215 0.009646861275 0.3104593324 0.9505376886 -1.971170444 0 0 0 1 ======================================================= The Registration Matrice in this Case Called "fslregistered.mat", using lta_convert we will make "fslregistered.lta" Command : lta_convert --infsl ./fsl/fslregistered.mat --outlta ./fsl/fslregistered.lta --src ./Image.nii --trg ./fsl/fslregistered.nii.gz --ltavox2vox =============================================================================== fslregistered.lta : 9.551459550857544e-01 -2.368552237749100e-01 6.928230822086334e-02 -4.191513061523438e+00 3.551747798919678e-01 9.071001410484314e-01 -2.992758452892303e-01 -5.014381408691406e+00 1.157622877508402e-02 3.104593753814697e-01 9.505378007888794e-01 -1.971183776855469e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 2.2. FreeSurfer Commands: =============================================================================== Command : mri_robust_register --mov ./Image.nii --dst ./fsl_resampled.nii.gz --mapmov ./freesurfer.nii --lta freesurfer.lta --halfmov half-mov.nii --halfdst halfdst.nii --halfmovlta h1.lta --halfdstlta h2.lta --iscale --satit =============================================================================== freesurfer.lta : type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 87.0000 129.0000 106.0000 sigma = 10000.0000 1 4 4 9.550938606262207e-01 -2.369909435510635e-01 6.931482255458832e-02 -4.167178630828857e+00 3.553738296031952e-01 9.070160388946533e-01 -2.993661761283875e-01 -4.999662876129150e+00 1.163147203624249e-02 3.105554580688477e-01 9.505058526992798e-01 -2.000635147094727e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 ================================================================================ The Registration Matrice in this Case Called "freesurfer.lta", using lta_convert we will do the conversion and build the FSL-Space "freesurfer.mat" Command : lta_convert --inlta ./freesurfer/freesurfer.lta --outfsl ./freesurfer/freesurfer.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz ======================================================== freesurfer.mat : 0.95509410 -0.28438917 0.08317780 -5.00063801 0.29614490 0.90701610 -0.29936624 -4.99965954 0.00969290 0.31055552 0.95050597 -2.00067019 0.00000000 0.00000000 0.00000000 1.00000000 ================================================================================ 2.3. ANTs Commands: ================================================================================ Commands : antsRegistrationSyNQuick.sh -d 3 -f ./fsl_resampled.nii.gz -m ./Image.nii -o ants_ -t r Using the ConvertTransform File we will make the "ants.txt" Command : ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt ================================================================================ ants.txt: #Insight Transform File V1.0 #Transform 0 Transform: AffineTransform_double_3_3 Parameters: 0.9996357319973235 -0.01682948721742278 -0.021099091785527296 0.015864886388920783 0.9988573896699559 -0.045080156184165145 0.02183365965755943 0.04472900023162478 0.9987605357863502 -2.215029749904149 1.2122977228542815 -6.0667455324006445 FixedParameters: 5.195914900051355 -10.250280974097581 -6.670270481513606 ================================================================================ Using lta_convert we first make "ants.lta" Command: lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox ================================================================================ type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 1.0000 1 4 4 9.996357560157776e-01 -1.322073861956596e-02 1.819471642374992e-02 1.924201965332031e+00 2.019538544118404e-02 9.988574385643005e-01 -4.472899809479713e-02 3.623344421386719e+00 -2.531890943646431e-02 4.508015885949135e-02 9.987605214118958e-01 2.642463684082031e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 ================================================================================= Using the lta_convert we make the "ants.mat", the FSL-Spaced Registration matrix for ANTs Command: lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz ================================================================================= 0.99963582 -0.01586489 0.02183366 2.30903101 0.01682949 0.99885744 -0.04472899 3.62335658 -0.02109909 0.04508016 0.99876052 2.64244890 0.00000000 0.00000000 0.00000000 1.00000000 As we could see there are problems in 'ants.lta' and 'ants.mat', I'm not sure Yet but I Suspect that the "PSR" Orientation of the Image Which is a Left-handed coordination System may cause that because in Another Experiment with "LAS" these problem had been occured but in another "RAS" Image the lta_convertor worked precisely with no problem. The Registration Files are attached for More Information about Image's Geometry Sform's and Other ... Best, Yazdan On Mon, 25 Sept 2023 at 17:16, Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote: External Email - Use Caution Hi Yazdan, I’m trying to understand the issues. Can you specify the commands used to generate the matrices attached to your email? And give more details of the issues you are seeing? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Yazdan Rezaee Jouryabi Sent: Monday, September 25, 2023 1:49 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] lta_convert issue with ants Registration Matrix External Email - Use Caution Dear all, Hi for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR) for our case i will attach the "fsl.mat" (Desired Matrix) using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below: - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert Best Regards Yazdan Rezaee J P.S. 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