Hi Noga,
Could you elaborate on the issue you're experiencing with the LTA and send an example?
Thanks, Malte
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of noga.kertes@campus.technion.ac.il noga.kertes@campus.technion.ac.il Sent: Tuesday, October 8, 2024 05:06 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
External Email - Use Caution
Thanks You for the response!
Another issue I encountered was with the .lta file that is being generated using mri_synthmorph. I want to use the .lta file with mri_convert to transform some another image with the same transform. However, the .lta file that is being generated by mri_synthmorph contain only the transformation without any other imformation (like the .lta file that mri_robust_register generate)
The command I ran: mri_synthmorph -m rigid -t temp_trans.lta -o temp_moved.nii.gz temp_moving.nii.gz temp_target.nii.gz
Thanks! Noga ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, October 1, 2024 17:12 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1HvZ3tfDVTBTHYJC9wnYNUaCWBxCPEh_yB5HQNB2JSWlD80Dk-TcXLGdZm8yRy_tieFMp4swNmFN3ODeqRJoteKGjAk5rYQ-CiapREOKQ-Q5Smm5Y49WxXhijEbFR-jxr5HNSNSH3yH0GvL6XW2S9hmIob3YMFLs3CV83ScBQjWqr6tFOxR2utGteOMN0U7HcH-RcU8SJe1vM0wqd4U047DxdWESoDWiluTGkas9v_0FL7D84UX6z3HKYUWxDMxnrcK-WuRaYmSu8yJQvu2NZ5GOIKGduhyCN-PmZdpEkQtuy81eORxohjNaOAOuex7ioNPASrwMjqGdMEjLUUiSI1g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Yes, 3 translation, then 3 rotation, then 3 scale, then 3 shear The translations depend upon the coordinate system, so they are kind of arbitrary; they are simply the last column of the matrix in the LTA
On 10/1/2024 4:19 AM, noga.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:
External Email - Use Caution
Thanks you for the help!
I ran this command and got the following output:
-14.7814 8.24088 7.81518 0.998388 4.87218 3.29326 1 1 1 0 -7.45058e-09 -5.58794e-09
What does each number represent?
Are the first three numbers representing translations? If so, and if they are supposed to be in millimeters, the values seem excessively high, even though the actual translation appears to be much smaller. However, when inspecting the resulting image, the registration seems to have been successful. Do you have any thoughts on why it could happen?
Thanks again, Noga
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Monday, September 30, 2024 17:02 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1J52q-H-8YrKgC4MraUgYbyuk_pNsWLH07KCbcf3dtM-x3p520Qelg4fp_XtTrwwP1_Nkk5Ng48PHTyQgsTwUAhAQ4KSbZCYA2Ak87E2XmSbexQ0PWMPqwNyg2nfPQp_TUdzQe0pPuiWNKavrhaw4RTqnwHivdA-EJyyWTpm9Yp1LXREJIapPsWZJb2SR1tTn10owApXUmE_IDUvPQmdZJja4VUZWn-uCSp8WJJJaaneypk8Asjq2058Ka2v_2TamSqV6eXhMsPjpDfaXeLz3f0s_FmuM1vG2WMoytdTpH_3U_Srukm7fOwPmNBkoOhOSVZ3IvrK4y-J2casDB9R6RQ/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Use mri_coreg --mat2par file.lta
On 9/29/2024 5:48 AM, noga.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:
External Email - Use Caution
Hello FreeSurfer Developers, I am using mri_robust_register to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a .lta file. I need to extract the rigid parameters (3 rotation angles in degrees and 3 translation parameters in millimeters). However, the transformation in the file doesn't seem right, as the translation parameters appear to be very large (I assume the values in the last column of the transformation are in millimeters). The moved image doesn’t seem to translate by more than a few millimeters. Is there a command for converting the .lta file into rotation and translation parameters? If not, could you provide more information on how to manually convert it using the transformation in the .lta file? Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
Thank you, Noga
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lfOnGw3bS5KKsNK7mij82i0jPgeP7SF1g4EuAwrh-E4cPUGPwWkSs9BizXjDt7j12EsnbKYtgR21dsYWjVfGkDvoKt5eEjC_X_EMj3oZXdZth26Dh407tccKkIQCr7zoqUlF8fpRr0_dKowitDga-v0U35BOYd8XxkPw2dQF3pTAuDLZvujCZo1CJBRP-tTAfZOgZXpMSCPei7_r-5HRJ_mb-sENUduMge6rmeKO1i88EtRqG8L5owrJo7n9REzl4zHIpulm8-sALuI9WhqB0EJWuVg_1Sq9l57N4EG9gjTWz2cMeootLqQ-71MogkMKE-yFcMLz7k7iecpxBc2KZA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
External e-mail, be judicious when opening attachments or links
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/11mTDjo2bCYEk_s-1GlcL-tqvri2F99ahxZC8a8on_hK1WrblyN7LsQz1Iv9Cbpshmi0ShqNloFUdhNXEzf1iWA78qC02YAD3Gj8o3SOxVqeU3RwWbeN2wmotsfyWjFBzZKQwpcsbWeseslBtAwezzRI9XVNhGFaWvBE_NmpEC7mD8uooc0B93U7L888FbUakHgeNm74WQmFuEo7yVQhOGhw65fUoz2DXVkDzgwezTFXcSX7CVfMRYultD764-GtSzlPVRTUUizaTgU4ItrQAa5_1htnBPTp49sZ0OToewPJ0yi9oRk0BZI_32s4IX0hhI5OTpcOpNJJyfx5lBL6AIw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
External e-mail, be judicious when opening attachments or links