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noga.kertes＠campus.technion.ac.il

29 Sep 2024 29 Sep '24

5:48 a.m.

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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

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Douglas N. Greve

30 Sep 30 Sep

10:02 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

Use mri_coreg --mat2par file.lta

On 9/29/2024 5:48 AM, noga.kertes@campus.technion.ac.il wrote:

...

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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

noga.kertes＠campus.technion.ac.il

1 Oct 1 Oct

4:19 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Monday, September 30, 2024 17:02 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/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:

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Thank you, Noga

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Douglas N. Greve

10:12 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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.il wrote:

...

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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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* Monday, September 30, 2024 17:02 *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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Use mri_coreg --mat2par file.lta

On 9/29/2024 5:48 AM, noga.kertes@campus.technion.ac.il mailto:noga.kertes@campus.technion.ac.il wrote:

...
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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* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://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

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noga.kertes＠campus.technion.ac.il

8 Oct 8 Oct

5:06 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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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:

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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?

Thanks again, Noga

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto: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.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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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:

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Thank you, Noga

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Hoffmann, Malte,PhD

8:22 p.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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

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Thanks You for the response!

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

On 10/1/2024 4:19 AM, noga.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:

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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?

Thanks again, Noga

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:

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Thank you, Noga

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noga.kertes＠campus.technion.ac.il

9 Oct 9 Oct

3:57 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoffmann, Malte,PhD MHOFFMANN@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

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Hi Noga,

Could you elaborate on the issue you're experiencing with the LTA and send an example?

Thanks, Malte

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Thanks You for the response!

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

You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important<https://secure-web.cisco.com/1AcPEV8m7x6tyhBqPAfeUlwhX9UJNrXMNs5cv1l5u4KMdCj...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.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:

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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?

Thanks again, Noga

You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is important<https://secure-web.cisco.com/1xFkyp-VW9JnWLhWX-CssnIifAWhnVE-uWL4xCtFePvwI47...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.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:

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Thank you, Noga

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Hoffmann, Malte,PhD

10:07 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

I am not sure what happened, but it looks like `mri_convert` doesn't like the shear in your voxel-to-world matrix. Any chance you can share the input images and mask? The LTA didn't make it to my side, as it was likely removed by the mailing list.

________________________________________ 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: Wednesday, October 9, 2024 03:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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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:

And the temp_moved_mask.nii.gz is not generated

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Hi Noga,

Could you elaborate on the issue you're experiencing with the LTA and send an example?

Thanks, Malte

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Thanks You for the response!

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

You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HvZ3tfDVTBTHYJC9wnYNUaCWBxCPEh_yB5HQNB2JSWlD80...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.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:

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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?

Thanks again, Noga

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:

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Thank you, Noga

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noga.kertes＠campus.technion.ac.il

11:57 a.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

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Sorry, I forgot to attached it. Target, moving, moving_mask and the .lta file are attached

Thank you! Noga

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu Sent: Wednesday, October 9, 2024 17:07 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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________________________________________ 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: Wednesday, October 9, 2024 03:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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:

And the temp_moved_mask.nii.gz is not generated

[You don't often get email from mhoffmann@mgh.harvard.edu. Learn why this is important at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1SC4VOR7LS4TOcVCFvfTkfKY_FZZH7lZK3s5JMe2khbKUvG...https://secure-web.cisco.com/1wEGmcHea3wPJbeJMb13U26_UyghkZ1rqr0u0dIhReWBLRc8IO35WxHRxx-Q5uyn34sHRheRLa-Z-QRU2Rxol08fys1Text1NsNQ1lYvFIkahj-aRZ5JRiQiVgiy4zdpUJjg36ELdbOfMyFdF8QqsImqYhEI1ODZXnnbcaPxyWSGDNxQuLpM9J78M5DzxzQruHx-tGc5rGrSHbBnMyqV1ZBnz1NmmaOyTZKLAZ3VwJXBNtQZNAXq54rRJPhjFIqbiZzPEPYhz6SdxCM1ntGQHiafm2lXAMrIgjSb6pTI2AFhtqZyxaS3nQf3ImZ1V8zPb/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F19NIoews75g1MQJ7WWQgztI5gweAmpQkQi8uHDJfmZXHSP8HUGH7_bvQqUTEoz8xzbjxP56p3EiZLA6ji9SEemJ4O-GthL3LJMbFzgaz4xipjMcvKQwQE-j0FffyMTy9EAFDolsrScpDPxWOpYTQiFyU8ZZAzcLuoHjuTDkEhDocW2_upcuLthXs27wEKw5KgVxqh5bCjcHOs7zgksXz57BO7YzY29NZOYBEryExu7u_IyOhx-0MOuK1Hj1w61Ktfvjv_yjRqi52ZdQnUGByxw05qfod0AjqE1lHOxm19jsfrAMfUbpD2ht3X0DCK28R-AFTKQfi97SC0C_zX8JGIcg%252Fhttps%25253A%25252F%25252Faka.ms%25252FLearnAboutSenderIdentification%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087421907%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DhbEkqPBFqr1ydE1cDiXYGg3HzPem4b9lZVaK4lqicg0%253D%26reserved%3D0 https://secure-web.cisco.com/1g0suNpRsE3SqktxYmS6TVd0ThUKdE7KZfHd5jP2z74gD1AMe99LlT7VggOJqq482kkBmLDKiKp6l-ffA-KoLPP36SszFAEt1e-PjrEueGvaSM4Wyy7ie9LKy7_inu0EwakzzXqvJoUxaWpky3v6Z6AieSfGlRWOy9o9nBasc_iYKeTIVY6DqRrH_xRpdsPTs8m1FAMkKWZ3S9PKwqj4Nm5IEDmKqj3a7XmY9RPeCzIsFSGYQLMAp3Rv95F9yEtrXvJsQ6b8m2L81LC8HTtSQoGKcykfmPyZeNyR7VgunjK9W0W2jxqZ6MrlfjJC2u5L0/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification%253Chttps%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F19NIoews75g1MQJ7WWQgztI5gweAmpQkQi8uHDJfmZXHSP8HUGH7_bvQqUTEoz8xzbjxP56p3EiZLA6ji9SEemJ4O-GthL3LJMbFzgaz4xipjMcvKQwQE-j0FffyMTy9EAFDolsrScpDPxWOpYTQiFyU8ZZAzcLuoHjuTDkEhDocW2_upcuLthXs27wEKw5KgVxqh5bCjcHOs7zgksXz57BO7YzY29NZOYBEryExu7u_IyOhx-0MOuK1Hj1w61Ktfvjv_yjRqi52ZdQnUGByxw05qfod0AjqE1lHOxm19jsfrAMfUbpD2ht3X0DCK28R-AFTKQfi97SC0C_zX8JGIcg%252Fhttps%25253A%25252F%25252Faka.ms%25252FLearnAboutSenderIdentification%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087421907%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DhbEkqPBFqr1ydE1cDiXYGg3HzPem4b9lZVaK4lqicg0%253D%26reserved%3D0%253E ]

Hi Noga,

Could you elaborate on the issue you're experiencing with the LTA and send an example?

Thanks, Malte

External Email - Use Caution

Thanks You for the response!

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

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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?

Thanks again, Noga

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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:

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1AKMNDpS_aPYP7UkbR4j-ZLukIOOhmiQ4GwtObDyAWA-V5B...https://secure-web.cisco.com/1iu_dZ2GqHoqj1wMR_QaZt-ej_TjmFyjQbcxWOFDuvkATDLsbRUOpxKjzfhYxyj8B4L3wbO7Pa-v_y9_y6J7NadAlWcWe6N4iC7oJ5s1FrLfYFxIJrapmfQGB5biKt2whePkGUQFQ6P3Dp5e70Dzc_Y0d98eaHFqOxqzDbDzMBtfa6aPKSWiZrr0GNUHO5qUccKN_itXnbTfOIBIdZvhyhxNRw997-lAtY8sDGwWWw1S8_Cq5jo1c4oYgRREz80CduUxLlcvQJeQ9Q9OPCwljm2o8c2mRAzoa7Iy3urg-1tmNJ4UaI9U_qsHwnkcxFdY6/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1lfOnGw3bS5KKsNK7mij82i0jPgeP7SF1g4EuAwrh-E4cPUGPwWkSs9BizXjDt7j12EsnbKYtgR21dsYWjVfGkDvoKt5eEjC_X_EMj3oZXdZth26Dh407tccKkIQCr7zoqUlF8fpRr0_dKowitDga-v0U35BOYd8XxkPw2dQF3pTAuDLZvujCZo1CJBRP-tTAfZOgZXpMSCPei7_r-5HRJ_mb-sENUduMge6rmeKO1i88EtRqG8L5owrJo7n9REzl4zHIpulm8-sALuI9WhqB0EJWuVg_1Sq9l57N4EG9gjTWz2cMeootLqQ-71MogkMKE-yFcMLz7k7iecpxBc2KZA%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087513153%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DXVbn502SW70dgM5a%252BIwisi%252FZcF50QqU7YLJ7%252FNyXbi4%253D%26reserved%3D0 https://secure-web.cisco.com/1W52cbmSoTOW6y43JbATW8hBFF0g5RGHJH5ayfUjmK5uduNroHPEIqsKTxqESH74mBbBny1A4AqlbSxB4l2nFfFTjiu6mevAMc023P5S0RHfx4NUZIMnA-8Bi5TPbyd8DEjwK7fJRfId33u3uzXTO8TUX4H2n-zJvh-kxb4Q6ZZlt56iE5zW6HEBtcC8tBD6VlXmUW8bV8eA1JWgPkt_vHUOGiz-o7mr7sw8gan_mz9pOI-0S6eirMTMPKtlm5kberb4hjk5AKHpavwa66nu9zA628dnknXV-1H9xkuLEbyyt93wfIguDieP7_qcoytf9/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qpWRxYCF7CxlD7UIdyxVPtf6d6ewZwf12Em0R_md1TxREEdC67je4lIgtnMykpEMtnprxVtArnaWLWDxURl4I0ULxqcYoZBcfjx-pa3V8tZG5ZCfoPc-HsM4DLEWj0_M7aeX46d-1xnth9U66BYV2vRgfWRLiSdq3i2nFkttLhYFClsZ6IBovbv85s-Uu3t8uxl7k03C2mTErsmo1f8rtUil6XlEG0jWdyLBmd_7nj02MtiSergqvKnWvgcZcBUIum2JiWZcA4GnbiE1p3iR8DdDqkfegBQaWgByu0bJ4p9Twumcat_lk2_Z1DiXiuuOZFuD8U48NZ8Y0vdgVrvntw%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087527709%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DhbRl0xPD8axqoQY49ctRZ0fCFPIGUa%252Bm1shlSR7akDk%253D%26reserved%3D0 https://secure-web.cisco.com/1vG8Oolj00APri8FLM64bkeYsVJPoq8CwDkRX3b-uxqBq5_t6-gAFzfk2VEPvuBZAAZkd7FJ95DKT4oT2fhvOUZXs-eTHV7rsJAZ5ndCGsx2-wfi6auUw0sTVmyXXEFlgMt7OkRHXgc4HT-lL65Lj8tJNJih2dy2_9WLm5aj8GcDgEnC4wIich5rag-GyGce87xBTrQTg80aKNy4cVMfuTYo84rCtVGrMNPth8N30a1xLD6h_mwzYHAOsNqrtKN50ndxV1mCUV68CIL9vUGga6wR0ekuX8f3RCdSzEBgG_nBlXwrUTDBkVRrL0VBNnhsx/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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_______________________________________________ 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11ED_KYLOPHC0CEpCQK1t4qNkCAS2zdikTAgBSTP1dZBBK4...https://secure-web.cisco.com/16etZQdGYQifgfleOvdp_Al8GXWf0-ip9GMv6ylDln7CVYxalR-aay8X0EM2avb9q30p1kZhfrHndKNbHoAZBOciMCbqTUlcVEUiSvB4PjcFWuHx85AC0s5dpUqSmtjicyR6PA3iJyol20HS7ZBk9KAJB4OrJfZhfkweGVRYr1pOPjC0NfGbeeUrp392Ohu7F5j5hv52yDyxrMi7_bOizbUeX1hW9sYZBacsbAZiYy6-Sx2QQkoYPhtC9P69SNCZEQBz4ke2GPhqyixJsWofsjdH1z-gRlG5-WfpMfWnvPwOzPqoOOt2Aa3LWtsHTldzA/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11mTDjo2bCYEk_s-1GlcL-tqvri2F99ahxZC8a8on_hK1WrblyN7LsQz1Iv9Cbpshmi0ShqNloFUdhNXEzf1iWA78qC02YAD3Gj8o3SOxVqeU3RwWbeN2wmotsfyWjFBzZKQwpcsbWeseslBtAwezzRI9XVNhGFaWvBE_NmpEC7mD8uooc0B93U7L888FbUakHgeNm74WQmFuEo7yVQhOGhw65fUoz2DXVkDzgwezTFXcSX7CVfMRYultD764-GtSzlPVRTUUizaTgU4ItrQAa5_1htnBPTp49sZ0OToewPJ0yi9oRk0BZI_32s4IX0hhI5OTpcOpNJJyfx5lBL6AIw%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087558396%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DYbVYkd5P3jW2lzPuTDE5Bv%252BcfZz3xqaxItmv8NFy5%252FM%253D%26reserved%3D0 https://secure-web.cisco.com/1vOTrA9JckmlOaZGTPoF3QihLW8QvyV44GfH-0vifVUYNYjYxDE1GvGvkTUH84ao3uq_kGJyEkRIckKOfR2V4WUmKRAxy3MbOh2sOMWGC_DfNkcDdmfKQq3mdA_16lwLUZqiFnYxue3K_jjgdIb8568XIjCqsbKeTvhJVhegpyWL7PiOvJn-CjbY_rFzJY7CvVaeQGtcB45ixf3et12aL_ZtOVogaH5zl7NR8CVqvmmSM-8LEV4sFhxSr8yc1vKTU5PmkcUjNfTqFqSPh0drzjD97U7sO556lw6q6A_LV-KmG00109DaHesoyHsTHxVOh/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qpWRxYCF7CxlD7UIdyxVPtf6d6ewZwf12Em0R_md1TxREEdC67je4lIgtnMykpEMtnprxVtArnaWLWDxURl4I0ULxqcYoZBcfjx-pa3V8tZG5ZCfoPc-HsM4DLEWj0_M7aeX46d-1xnth9U66BYV2vRgfWRLiSdq3i2nFkttLhYFClsZ6IBovbv85s-Uu3t8uxl7k03C2mTErsmo1f8rtUil6XlEG0jWdyLBmd_7nj02MtiSergqvKnWvgcZcBUIum2JiWZcA4GnbiE1p3iR8DdDqkfegBQaWgByu0bJ4p9Twumcat_lk2_Z1DiXiuuOZFuD8U48NZ8Y0vdgVrvntw%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087572960%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DfspJrWt8OGz801FqEjf4qyoyjxNDS%252B%252BxelUzFIR279s%253D%26reserved%3D0 https://secure-web.cisco.com/1vG8Oolj00APri8FLM64bkeYsVJPoq8CwDkRX3b-uxqBq5_t6-gAFzfk2VEPvuBZAAZkd7FJ95DKT4oT2fhvOUZXs-eTHV7rsJAZ5ndCGsx2-wfi6auUw0sTVmyXXEFlgMt7OkRHXgc4HT-lL65Lj8tJNJih2dy2_9WLm5aj8GcDgEnC4wIich5rag-GyGce87xBTrQTg80aKNy4cVMfuTYo84rCtVGrMNPth8N30a1xLD6h_mwzYHAOsNqrtKN50ndxV1mCUV68CIL9vUGga6wR0ekuX8f3RCdSzEBgG_nBlXwrUTDBkVRrL0VBNnhsx/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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_______________________________________________ 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/1R95C_Yo_K-5fnPux9DaFz6TiJS5lqAoug4-PClLqKmj2CH...https://secure-web.cisco.com/1bsZAi5pEhPEg_QvM2dPeK1NLMlrTSmwK54jKhQ1HF4nd05vs5Aw7zGEBabYxk3GpEH9uu_1NNtfmyNLsyWfLHlfp_m0kREUHbCc-JWBd8RjgB_-gCoYbJcU_eXVRGjI79lvlAQ2gkZROh1j41jeUdWRHS-PDvouwSKfykndiY-_pVdIuPdKqoBIsH79Vvv8DTxh1olHerIs8aJSEiMzrCbp_zX77Or5B-ZaIVGpbiN90zeWI7oRCVpSC5MNMxbixf2BQZgqVG_Vv7FoeYJN7iMqw1yd56BE2fKp1k3EdKTs4fFiJXpekMHsIzysxYNXa/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qpWRxYCF7CxlD7UIdyxVPtf6d6ewZwf12Em0R_md1TxREEdC67je4lIgtnMykpEMtnprxVtArnaWLWDxURl4I0ULxqcYoZBcfjx-pa3V8tZG5ZCfoPc-HsM4DLEWj0_M7aeX46d-1xnth9U66BYV2vRgfWRLiSdq3i2nFkttLhYFClsZ6IBovbv85s-Uu3t8uxl7k03C2mTErsmo1f8rtUil6XlEG0jWdyLBmd_7nj02MtiSergqvKnWvgcZcBUIum2JiWZcA4GnbiE1p3iR8DdDqkfegBQaWgByu0bJ4p9Twumcat_lk2_Z1DiXiuuOZFuD8U48NZ8Y0vdgVrvntw%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087719317%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3D4aJlVls17bRqmw1Vb%252BybnM8ZXqApLXFQ66pppuE5Gr4%253D%26reserved%3D0 https://secure-web.cisco.com/1vG8Oolj00APri8FLM64bkeYsVJPoq8CwDkRX3b-uxqBq5_t6-gAFzfk2VEPvuBZAAZkd7FJ95DKT4oT2fhvOUZXs-eTHV7rsJAZ5ndCGsx2-wfi6auUw0sTVmyXXEFlgMt7OkRHXgc4HT-lL65Lj8tJNJih2dy2_9WLm5aj8GcDgEnC4wIich5rag-GyGce87xBTrQTg80aKNy4cVMfuTYo84rCtVGrMNPth8N30a1xLD6h_mwzYHAOsNqrtKN50ndxV1mCUV68CIL9vUGga6wR0ekuX8f3RCdSzEBgG_nBlXwrUTDBkVRrL0VBNnhsx/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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nw1q1SoGHcFALIB9HZbD1Faa0CTlSGK5unNqqXNv3MNr8m...https://secure-web.cisco.com/1HUetW4WWSB9XxaJ2AAvYJ3Tx3vcOq07RD33fQOJpJ70QEa56yPecdxhQQCm-KWDgdH75KImHyflZgIV5AdSPHvLsVafQm0md8PWV3Ubt0oQIBhvjrI5zIsYMLtetHP1T8nqRHUH3n4rTLL8pKLALlnq3MyvuOPodMhvV5bD7ni7CHnlOpKk6vPYTkS7zlYegjFBVKaIUjCMDEl3B2JZCx7MSO5uks8l-5a_aVe0OuZHeo6FcHN665UFahOdb2wZhgk-u3ZF4Khidkh3MzfzfHduXMhTPwyAFMLhGEv4-GNe_7tQEXmSf51oGaFdKjHkQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F12oE71QGGELoBj-2CErgGB63h7uJUCjpX5HW4oy6b-NqvPkt0ebfnSc4b-21VWL7LeSdScpVyPcv8UDuDiOpIAtauHVmICLY9deppj5Ij1LemYodulSTPky_RupUj9KWTY57-ma0QcyCQErqCZeNDJlMeJKYlF8og0_0gWFCU-p6mNVNjMc0UkX5dekJuIt61yTehbJ9q2VOnAtQ1wKgwbBR8gs5qunnzQIzCxNxiDcqrp_p5AfJfJqTEStw8r-UXqjQdvTQoXSAUIgte3unwI1EU8DEDZlgrBDcwc5XR_UL5A3DV_xXA2SHuVC35S2P65MeQEsIsg6IZ8cZy86yYVw%252Fhttps%25253A%25252F%25252Fwww.massgeneralbrigham.org%25252Fcomplianceline%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087746644%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DcViarVGiDhFrKtLFfIZ%252F4ACQEcxwvJ91tseJr4lvKgI%253D%26reserved%3D0 https://secure-web.cisco.com/1qjDkzIP6hOPQy5L2ztBfsWRkAKz3SM4-FNCT0HeW0cfmbWAofJ9z48isDSH7B-ZnVUTBrCCndcKEELNCLRd7H9CeZqsK3Zbpe4VaKigawuFo0AYq3OeiOw52A3b4s7_31g8jNb1ZsVLonf-YnaHc7-vIVuhi7cjPl1HLcLDar7dG8vWXIVr-j6_EpnqGDYxb6oZbysdvUa0zqFsBHnToyxJwnVCO3u-chU17GpUAdpGSfk4fR5omvcjdztJqV_XZrPQHDGzQ-leiEALrMl65aG1ZKkKiU5kmzt5-ISVS6Z9OcdN7tslTKxxCqfnYU1sV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Vx5DtmrpbXvMGH9JeNf6lTSyrabeFNkeV-h90Js-M_3DM4...https://secure-web.cisco.com/1fnviu4DxJGk2fUhc07IVcbO-XwY_5qjb1AeLi3gOdNaZY6vUJki8FF3vOrcAmjiHViWDq0DHf8iP_7D_xIaqhLnxIUSHEWHsPDQhLwqYAukevhUzBE2ZR9zqlWbEiGKabhf9JQIgAjzY_uz9BDP0xCPG_D3xDejhvzYg3K8FWQS98xzyG5dobMf1VP0v3WuAUiZpvD1T-7fX9Getuf3TUA7wBUzfldyxvZK-7kaSA9g7uQ0K2JcyweMb-RyzDwfI7NDhTtQiTJNBTn-NdbN3Hjf2PCWYUPsb1-7cUxYJzbA-SsQks5CJnYF8oj2YWUds/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F12oE71QGGELoBj-2CErgGB63h7uJUCjpX5HW4oy6b-NqvPkt0ebfnSc4b-21VWL7LeSdScpVyPcv8UDuDiOpIAtauHVmICLY9deppj5Ij1LemYodulSTPky_RupUj9KWTY57-ma0QcyCQErqCZeNDJlMeJKYlF8og0_0gWFCU-p6mNVNjMc0UkX5dekJuIt61yTehbJ9q2VOnAtQ1wKgwbBR8gs5qunnzQIzCxNxiDcqrp_p5AfJfJqTEStw8r-UXqjQdvTQoXSAUIgte3unwI1EU8DEDZlgrBDcwc5XR_UL5A3DV_xXA2SHuVC35S2P65MeQEsIsg6IZ8cZy86yYVw%252Fhttps%25253A%25252F%25252Fwww.massgeneralbrigham.org%25252Fcomplianceline%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087774170%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3Dbl53LEQ1IIVNT%252F85Qz%252BDM4ObhMDqgzW1eY3io280nMw%253D%26reserved%3D0>https://secure-web.cisco.com/1qjDkzIP6hOPQy5L2ztBfsWRkAKz3SM4-FNCT0HeW0cfmbWAofJ9z48isDSH7B-ZnVUTBrCCndcKEELNCLRd7H9CeZqsK3Zbpe4VaKigawuFo0AYq3OeiOw52A3b4s7_31g8jNb1ZsVLonf-YnaHc7-vIVuhi7cjPl1HLcLDar7dG8vWXIVr-j6_EpnqGDYxb6oZbysdvUa0zqFsBHnToyxJwnVCO3u-chU17GpUAdpGSfk4fR5omvcjdztJqV_XZrPQHDGzQ-leiEALrMl65aG1ZKkKiU5kmzt5-ISVS6Z9OcdN7tslTKxxCqfnYU1sV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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Hoffmann, Malte,PhD

12:28 p.m.

New subject: FreeSurfer - extract rigid parameters from .lta file

Thanks for attaching the files. The transform you have there is in NiftyReg format and needs to be converted to LTA with `lta_convert --inniftyreg temp_trans.lta --outlta out.lta --src temp_moving.nii.gz --trg temp_target.nii.gz` before you can apply it with `mri_convert`.

SynthMorph's switch from NiftyReg to LTA format did note make it into FreeSurfer 7.4.1. It'll be in the FreeSurfer dev build, the upcoming 7.5 release, and the latest SynthMorph from the Docker Hub.

________________________________________ 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: Wednesday, October 9, 2024 11:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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Sorry, I forgot to attached it. Target, moving, moving_mask and the .lta file are attached

Thank you! Noga

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________________________________________ 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: Wednesday, October 9, 2024 03:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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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:

And the temp_moved_mask.nii.gz is not generated

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Hi Noga,

Could you elaborate on the issue you're experiencing with the LTA and send an example?

Thanks, Malte

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Thanks You for the response!

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

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On 10/1/2024 4:19 AM, noga.kertes@campus.technion.ac.ilmailto:noga.kertes@campus.technion.ac.il wrote:

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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?

Thanks again, Noga

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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:

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Thank you, Noga

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1qpWRxYCF7CxlD7UIdyxVPtf6d6ewZwf12Em0R_md1TxREEdC67je4lIgtnMykpEMtnprxVtArnaWLWDxURl4I0ULxqcYoZBcfjx-pa3V8tZG5ZCfoPc-HsM4DLEWj0_M7aeX46d-1xnth9U66BYV2vRgfWRLiSdq3i2nFkttLhYFClsZ6IBovbv85s-Uu3t8uxl7k03C2mTErsmo1f8rtUil6XlEG0jWdyLBmd_7nj02MtiSergqvKnWvgcZcBUIum2JiWZcA4GnbiE1p3iR8DdDqkfegBQaWgByu0bJ4p9Twumcat_lk2_Z1DiXiuuOZFuD8U48NZ8Y0vdgVrvntw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer https://secure-web.cisco.com/18WB58GRsxnrZBRkPtlSr0422XBPTNA3-BGd8n17BGOKI2PkTAOXdfZc_G7T2LBtlm-7voiNlsRC-Z_IG-EF3qebHmPGEhbMYuyP7GtCo7OHpG1Bc2Z7EMsdLOTuXElU3cixHgkQzbi5YCU-TwzpNPx6j9gxbyWCsg81Woo2-8XYMZAvEIsmLbSXFDEuJBSmBIMCLOFIl5LYovEbKjoi5WTabQEVkcSqQh-gzfRAXJCi4488gtsgcnjt0pIbyAEvNOinSr-EhzgZCrWXHzWC2_4wuqQln9GXVuVssgXdJ1ep8u7frvq0BMGmcsVWyksr-/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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/12oE71QGGELoBj-2CErgGB63h7uJUCjpX5HW4oy6b-NqvPkt0ebfnSc4b-21VWL7LeSdScpVyPcv8UDuDiOpIAtauHVmICLY9deppj5Ij1LemYodulSTPky_RupUj9KWTY57-ma0QcyCQErqCZeNDJlMeJKYlF8og0_0gWFCU-p6mNVNjMc0UkX5dekJuIt61yTehbJ9q2VOnAtQ1wKgwbBR8gs5qunnzQIzCxNxiDcqrp_p5AfJfJqTEStw8r-UXqjQdvTQoXSAUIgte3unwI1EU8DEDZlgrBDcwc5XR_UL5A3DV_xXA2SHuVC35S2P65MeQEsIsg6IZ8cZy86yYVw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline https://secure-web.cisco.com/1op9CSoMnb0KZpuvqLJxR17-aX1CPesKxVHCf0AxS6pp_0X2h05U0ItZBA7dzVVa1Wn8QC-fsjJTBrQx-b6EjKTdRgsILdw1745P4BbFzrEi4A2N8JC2d6kRb28Sbuyadbq6pI9PbdvKCGXE69CINWSuuH7gCGgf3dtN15lDc2h9VfMkWfso-lPRWWkIHh5KcpWnzgnxYQQZ3tjCDAxERKmw1lujkXbOEfqGOAtQxSHgOJqQye-9JRgYZvEQt-525J9nofsibVfcN6turVxw5J1KHtaedv4sXgNGzl5FnRYEYlWQ1iqiVK3vn-T8fxOUo/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/12oE71QGGELoBj-2CErgGB63h7uJUCjpX5HW4oy6b-NqvPkt0ebfnSc4b-21VWL7LeSdScpVyPcv8UDuDiOpIAtauHVmICLY9deppj5Ij1LemYodulSTPky_RupUj9KWTY57-ma0QcyCQErqCZeNDJlMeJKYlF8og0_0gWFCU-p6mNVNjMc0UkX5dekJuIt61yTehbJ9q2VOnAtQ1wKgwbBR8gs5qunnzQIzCxNxiDcqrp_p5AfJfJqTEStw8r-UXqjQdvTQoXSAUIgte3unwI1EU8DEDZlgrBDcwc5XR_UL5A3DV_xXA2SHuVC35S2P65MeQEsIsg6IZ8cZy86yYVw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>https://secure-web.cisco.com/1op9CSoMnb0KZpuvqLJxR17-aX1CPesKxVHCf0AxS6pp_0X2h05U0ItZBA7dzVVa1Wn8QC-fsjJTBrQx-b6EjKTdRgsILdw1745P4BbFzrEi4A2N8JC2d6kRb28Sbuyadbq6pI9PbdvKCGXE69CINWSuuH7gCGgf3dtN15lDc2h9VfMkWfso-lPRWWkIHh5KcpWnzgnxYQQZ3tjCDAxERKmw1lujkXbOEfqGOAtQxSHgOJqQye-9JRgYZvEQt-525J9nofsibVfcN6turVxw5J1KHtaedv4sXgNGzl5FnRYEYlWQ1iqiVK3vn-T8fxOUo/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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_______________________________________________ Freesurfer mailing list 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/freesurfer https://secure-web.cisco.com/18WB58GRsxnrZBRkPtlSr0422XBPTNA3-BGd8n17BGOKI2PkTAOXdfZc_G7T2LBtlm-7voiNlsRC-Z_IG-EF3qebHmPGEhbMYuyP7GtCo7OHpG1Bc2Z7EMsdLOTuXElU3cixHgkQzbi5YCU-TwzpNPx6j9gxbyWCsg81Woo2-8XYMZAvEIsmLbSXFDEuJBSmBIMCLOFIl5LYovEbKjoi5WTabQEVkcSqQh-gzfRAXJCi4488gtsgcnjt0pIbyAEvNOinSr-EhzgZCrWXHzWC2_4wuqQln9GXVuVssgXdJ1ep8u7frvq0BMGmcsVWyksr-/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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1op9CSoMnb0KZpuvqLJxR17-aX1CPesKxVHCf0AxS6pp_0X2h05U0ItZBA7dzVVa1Wn8QC-fsjJTBrQx-b6EjKTdRgsILdw1745P4BbFzrEi4A2N8JC2d6kRb28Sbuyadbq6pI9PbdvKCGXE69CINWSuuH7gCGgf3dtN15lDc2h9VfMkWfso-lPRWWkIHh5KcpWnzgnxYQQZ3tjCDAxERKmw1lujkXbOEfqGOAtQxSHgOJqQye-9JRgYZvEQt-525J9nofsibVfcN6turVxw5J1KHtaedv4sXgNGzl5FnRYEYlWQ1iqiVK3vn-T8fxOUo/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1op9CSoMnb0KZpuvqLJxR17-aX1CPesKxVHCf0AxS6pp_0X2h05U0ItZBA7dzVVa1Wn8QC-fsjJTBrQx-b6EjKTdRgsILdw1745P4BbFzrEi4A2N8JC2d6kRb28Sbuyadbq6pI9PbdvKCGXE69CINWSuuH7gCGgf3dtN15lDc2h9VfMkWfso-lPRWWkIHh5KcpWnzgnxYQQZ3tjCDAxERKmw1lujkXbOEfqGOAtQxSHgOJqQye-9JRgYZvEQt-525J9nofsibVfcN6turVxw5J1KHtaedv4sXgNGzl5FnRYEYlWQ1iqiVK3vn-T8fxOUo/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Douglas N. Greve
Hoffmann, Malte,PhD
noga.kertes＠campus.technion.ac.il