External Email - Use Caution Hi,
I want to use mri_synthmorph to rigid register a moving image to a fixed image therefore I ran the following command: mri_synthmorph -m rigid -t temp_trans.lta -o temp_moved.nii.gz temp_moving.nii.gz temp_target.nii.gz The file `temp_trans.lta` is attached. Afterwards, I want to use `temp_trans.lta` to register the mask of the moving image therefore I use mri_convert in the following way: `mri_convert -at temp_trans.lta temp_moving_mask.nii.gz temp_moved_mask.nii.gz -rt nearest` But the following error message appears: reading from temp_moving_mask.nii.gz... WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (1.172,1) (1.172,1) (1.5,1) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 0.00000; TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file temp_trans.lta... Reading transform with LTAreadEx() error: Cannot allocate memory error: LTAalloc(-240): could not allocate xforms And the temp_moved_mask.nii.gz is not generated Thanks, Noga ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoffmann, Malte,PhD <mhoffm...@mgh.harvard.edu> Sent: Wednesday, October 9, 2024 03:22 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file [You don't often get email from mhoffm...@mgh.harvard.edu. Learn why this is important at https://secure-web.cisco.com/19NIoews75g1MQJ7WWQgztI5gweAmpQkQi8uHDJfmZXHSP8HUGH7_bvQqUTEoz8xzbjxP56p3EiZLA6ji9SEemJ4O-GthL3LJMbFzgaz4xipjMcvKQwQE-j0FffyMTy9EAFDolsrScpDPxWOpYTQiFyU8ZZAzcLuoHjuTDkEhDocW2_upcuLthXs27wEKw5KgVxqh5bCjcHOs7zgksXz57BO7YzY29NZOYBEryExu7u_IyOhx-0MOuK1Hj1w61Ktfvjv_yjRqi52ZdQnUGByxw05qfod0AjqE1lHOxm19jsfrAMfUbpD2ht3X0DCK28R-AFTKQfi97SC0C_zX8JGIcg/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification ] Hi Noga, Could you elaborate on the issue you're experiencing with the LTA and send an example? Thanks, Malte ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of noga.ker...@campus.technion.ac.il <noga.ker...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@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 dgr...@mgh.harvard.edu. Learn why this is important<https://secure-web.cisco.com/1AcPEV8m7x6tyhBqPAfeUlwhX9UJNrXMNs5cv1l5u4KMdCjnkcsYSA7EvBZ3kc9uHyGzhZoO-Vu8KjQJcGDfWANkHVf5K86U3R61eavO3NQK4wd7ad9h9-7IwkxfOZmZUVIUNw9a74G1Brfr62lckvsI1BZ36gvWxAXcjXgVkQwBCKSgBzhEf0bCxNaE74pacLTRMWP4TqsIq-ahzF2dM1D_Z9sTyLmYteDtPaxOBBohcT1qH7MK-27rSJOC1Rv2fKG7SOKODE2EdDiI4k3GCa4Fr34ObsEaLEVRI_v9Bggcaiw0Pt_ttWM6VG30Jxe7P9bLdUWHlTzTiUqQPnJaXxw/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1HvZ3tfDVTBTHYJC9wnYNUaCWBxCPEh_yB5HQNB2JSWlD80Dk-TcXLGdZm8yRy_tieFMp4swNmFN3ODeqRJoteKGjAk5rYQ-CiapREOKQ-Q5Smm5Y49WxXhijEbFR-jxr5HNSNSH3yH0GvL6XW2S9hmIob3YMFLs3CV83ScBQjWqr6tFOxR2utGteOMN0U7HcH-RcU8SJe1vM0wqd4U047DxdWESoDWiluTGkas9v_0FL7D84UX6z3HKYUWxDMxnrcK-WuRaYmSu8yJQvu2NZ5GOIKGduhyCN-PmZdpEkQtuy81eORxohjNaOAOuex7ioNPASrwMjqGdMEjLUUiSI1g%252Fhttps%25253A%25252F%25252Faka.ms%25252FLearnAboutSenderIdentification%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Cc07f875ebcd049fcb88808dce7f8d49f%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640303135597776%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DNRQIWL7LPYi0HdThQtQVB5GCcyH43OAdriA0kHt%252F9ig%253D%26reserved%3D0<https://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.ker...@campus.technion.ac.il<mailto:noga.ker...@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-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 Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Monday, September 30, 2024 17:02 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file You don't often get email from dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>. Learn why this is important<https://secure-web.cisco.com/1xFkyp-VW9JnWLhWX-CssnIifAWhnVE-uWL4xCtFePvwI47sWksMuvC0fVuqTjUIseXnLa5VWmir6AXLcpJEQ57XS0YB8Kl0Nwx3PJSmIvRzXxQeAVKb44FMh7RHKA_6Etm4XuTH-HXk4IoNgK7iLz7UqGVDLITZS-ovg18kFS7_hxyfkf1zbEV0pljvw38h9F9JYvNBFSQAQJO8HAxB6X5ADKwsS_r1OEW2ccHGRPScbfcAs7cCBtRr05i1_1K4cvuhKhTY_bA47m2KNGQELSL3oIk2rcH00OHtiWzLt4pn5ZYplUpTSkuiIp2xafPepc7EHLpB-0g37a4Trn_AjWw/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1J52q-H-8YrKgC4MraUgYbyuk_pNsWLH07KCbcf3dtM-x3p520Qelg4fp_XtTrwwP1_Nkk5Ng48PHTyQgsTwUAhAQ4KSbZCYA2Ak87E2XmSbexQ0PWMPqwNyg2nfPQp_TUdzQe0pPuiWNKavrhaw4RTqnwHivdA-EJyyWTpm9Yp1LXREJIapPsWZJb2SR1tTn10owApXUmE_IDUvPQmdZJja4VUZWn-uCSp8WJJJaaneypk8Asjq2058Ka2v_2TamSqV6eXhMsPjpDfaXeLz3f0s_FmuM1vG2WMoytdTpH_3U_Srukm7fOwPmNBkoOhOSVZ3IvrK4y-J2casDB9R6RQ%252Fhttps%25253A%25252F%25252Faka.ms%25252FLearnAboutSenderIdentification%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Cc07f875ebcd049fcb88808dce7f8d49f%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640303135617415%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3D5FkGr%252Bt%252FMNhdqU3j9c84JCBklnLxizmWEguVwqUorLc%253D%26reserved%3D0<https://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.ker...@campus.technion.ac.il<mailto:noga.ker...@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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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