External Email - Use Caution Hi Yujing, 90 I mean that i had use "lta_convert" in two setup, 1) Images in RAS Orientation (Worked Well) 2) Images in "LAS/PSR" Orientation (Issues Happened here)
and Yes By definition nii, is defined in RAS+ so if we take a look at T_Vox2anatomical (S_rows (Sform), or quaternions (qform)) Which are stored in the header we could interpret it as mri_info does too, and says that all are in LAS orientation. I thought that as "LAS-PSR" both are left-handed coordinate systems the program might have some issues with this Type of orientation and work Ok with right handed Images. The Second guess might be usage of S-forms by one program and qform by the Other one. as it is stated here https://secure-web.cisco.com/1-25w9APT0HgxT9N-EfI7mMc3icOz7cv81LXfb_b6INmne_im6mecYchK5o1PgjqsRZQIEzmSWA766gUHOTCdLvIwzLktoBT-Rlp4l87WHrmPX40RSFj2HZxI0CrNYrNagtsOTi7NFKCGmc2D9pZ9p2lGke0mrCuvNRI8s86bvbnDMQag74pfLgQ_Of_bLPihtwfBDsPWONScTzAS_KYxraEHCZB1Y4425Ywy6808FDm_Lk5e64mtQlRKeS2zu0no30bjVGZy3dxATEP-I0Q11v_zy8uv0zL0Z6NDw90MT4td7k3w-r6hd1QySOc4vUTI5LKr2GL0aM8PnDJyXs5EHQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55547.html Best, Yazdan On Thu, 12 Oct 2023 at 18:22, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > 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 (*MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1Ge3sBzHTtpKPPBh9OiSTIgwYz1_Beh4d9YQJtgo5XKYxA26D8XNEFTLbdY1PsOTpom82rAHYDzOL7jiDVXzsfOk7EQ_Afuse434ESbq411FI8DV1o3Sh2NZ3Ke5QHOSKBvNxOKxF8xyaQPDKNFI1PE6WDHeWhcWNeTSsYmmBpk3i7_1TBwmQ6n1XqVH-IwJMHFOmuSbtrsGHwWnj7LV4ZD4huv_yp8b777ivopbUP6AY99fHLyniraYrPhMJWD0rT7gbtUkaNng_SckMJf8EHsHpyWpx1O7hNvClYt9LD4DJq_Ry9s2RExRiWJpi90t2_8PTxfSPMbLsFTyh0ak5KA/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F71441883%2Fhow-to-get-transformation-affine-from-itk-registration > <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> > 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 < > 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> > *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> > 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 < > 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 > *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. *" I've checked the one similar mail on this topic and the > conclusion on that was about (sform, qform) incompatibility but the affine > matrices of S-form and q-form are equivalent in my case." > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1EVZ_Jd_TjO8poEPWsnM3wvJ0Smw49A19G1e3bgBHgbzDMjnQJ0z3TaXrhUgJuCld9ehirNHJ_N0jIrHTffM5DPs1NmDt150dKU_W6GgRtPlFLBMvOLLfiOxebSRY4goXhMEhblTcGR1X1I38YDF6lp04K5X0lkvxyh_VEULPSuMNYVp7w0JY3yr_uOEBK61RO2-3VAEEwNEiC78GuRbTjNKM2dpKYsggTuwZt0s-6cx69x5XsrLDFH3QuUlMOmHNwdDuIIILduwKar-H74X1gGBqtQPvHDHq_sfE84lYUUgJ07JbKquwHCKqb0b4KP9B/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1CVysUaKA0QPJhHH2wwhYBipzUhFEaeL8kkwOtuATULgzm-ARVtRifTqrnuMch9mPrhoX5WsrgJCZI4n6LV0QrBOiwz8JOJSZcKXl0-srjhHE7Ez1eAdpgDrWIqslv1yZuu9lDDu4UrcCR_1k8-OHZM1lX5im7TD25ziCO5ibM6spWh-yZJ_pdgSrOWg3COhe2JLUiyCL3VPWaa-l3gJ-VY8E3fKgFi47mdINsuywYT2Z2bpFzMA0qVMOcxBZP6V2Jz-SpyfFbeS55S0r_f_lNm2JigMyuajjviAgHw-npf_6HYFs541IzQp4hzn0kOTN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > The information in this e-mail is intended only for the person to whom it > is addressed. 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