External Email - Use Caution
Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time! Mirsol
You can try lta_convert.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mirsol Choi Sent: Wednesday, November 29, 2023 5:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time! Mirsol
External Email - Use Caution
Hi Yujing,
I really appreciate your quick response.
The following is the error I get when I try to perform this:
Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat --outreg reg.lta
7.4.1
--inreg: register.dat input TK REG transform.
--outreg: reg.lta output reg.dat matrix.
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
error: corRead(): can't open file /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info
ERROR readREG: cannot read src MRI
Mirsols-MacBook-Pro:dtrecon mirsolchoi$
Is there an additional file I need to complete this process?
Thank you so much for your time.
Mirsol
On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
You can try lta_convert.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi *Sent:* Wednesday, November 29, 2023 5:19 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution *Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time!
Mirsol _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rP... 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 https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHC... < https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHC... . 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.
Try to specify –src <> and –trg <> --src specify src image geometry (mov volume for TKREG/register.dat) --trg specify trg image geometry
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mirsol Choi Sent: Wednesday, November 29, 2023 5:32 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hi Yujing,
I really appreciate your quick response.
The following is the error I get when I try to perform this:
Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat --outreg reg.lta
7.4.1
--inreg: register.dat input TK REG transform.
--outreg: reg.lta output reg.dat matrix.
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
error: corRead(): can't open file /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info
ERROR readREG: cannot read src MRI
Mirsols-MacBook-Pro:dtrecon mirsolchoi$
Is there an additional file I need to complete this process?
Thank you so much for your time.
Mirsol
On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: You can try lta_convert.
Best,
Yujing
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 Mirsol Choi Sent: Wednesday, November 29, 2023 5:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time! Mirsol _______________________________________________ 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/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rPNfZCqlx1FynjTqlfu6S34aqEatZuKRZs2wr1dsd3zdLiZfXiS--s-au26O8n4vYtdS6hTZXPRmbMwsKgPOUyBhzwRzfmpj2e504WULnnxGgg2aDR4zWxspSKN1E3FoVpyfnSr3vL_SJonRCVW-ENaJOrNlbAFTvjQ5VkSP3Wx_xCte0P8BNZT6d5mOtTFCF20ckxPDDWTPfvGIfXWvBIZnJ2HE8790vLymblOd5h7fRMDT8ZnEuBN5vEZscSF_RB1_xVNelSTyepz1mdP6dWClmntOFYOTkvfQtFdwxw/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/compliancelinehttps://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/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/compliancelinehttps://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/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.
External Email - Use Caution
Hi Yujing,
Thanks again for your quick response.
For src image, do you mean the file that I used to generate the original register.dat file? For instance, the register.dat file was produced by running dt_recon (using input of dti.nii.gz).
Is this dti.nii.gz for file I should use for correct conversion to reg.lta?
Thank you! M
On Wed, Nov 29, 2023 at 3:40 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Try to specify –src <> and –trg <>
--src
specify src image geometry (mov volume for TKREG/register.dat)--trg
specify trg image geometry*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi *Sent:* Wednesday, November 29, 2023 5:32 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution *Hi Yujing,
I really appreciate your quick response.
The following is the error I get when I try to perform this:
Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat --outreg reg.lta
7.4.1
--inreg: register.dat input TK REG transform.
--outreg: reg.lta output reg.dat matrix.
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
error: corRead(): can't open file /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info
ERROR readREG: cannot read src MRI
Mirsols-MacBook-Pro:dtrecon mirsolchoi$
Is there an additional file I need to complete this process?
Thank you so much for your time.
Mirsol
On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
You can try lta_convert.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi *Sent:* Wednesday, November 29, 2023 5:19 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution *Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time!
Mirsol
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/1U-iwgipV7SsqgXQL-zgbDVJqpHaIRbL1c5gz95C4fRVuka... https://secure-web.cisco.com/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rPNfZCqlx1FynjTqlfu6S34aqEatZuKRZs2wr1dsd3zdLiZfXiS--s-au26O8n4vYtdS6hTZXPRmbMwsKgPOUyBhzwRzfmpj2e504WULnnxGgg2aDR4zWxspSKN1E3FoVpyfnSr3vL_SJonRCVW-ENaJOrNlbAFTvjQ5VkSP3Wx_xCte0P8BNZT6d5mOtTFCF20ckxPDDWTPfvGIfXWvBIZnJ2HE8790vLymblOd5h7fRMDT8ZnEuBN5vEZscSF_RB1_xVNelSTyepz1mdP6dWClmntOFYOTkvfQtFdwxw/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/13WPJxA1Btfx5KYlK6mbOcr9MFjhpgowxsgpuxyLvgs7eDv... https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/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/13WPJxA1Btfx5KYlK6mbOcr9MFjhpgowxsgpuxyLvgs7eDv... https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1U-iwgipV7SsqgXQL-zgbDVJqpHaIRbL1c5gz95C4fRVuka... 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 https://secure-web.cisco.com/13WPJxA1Btfx5KYlK6mbOcr9MFjhpgowxsgpuxyLvgs7eDv... < https://secure-web.cisco.com/13WPJxA1Btfx5KYlK6mbOcr9MFjhpgowxsgpuxyLvgs7eDv... . 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.
Src image is the movable image that is mapped to target image.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mirsol Choi Sent: Wednesday, November 29, 2023 5:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hi Yujing,
Thanks again for your quick response.
For src image, do you mean the file that I used to generate the original register.dat file? For instance, the register.dat file was produced by running dt_recon (using input of dti.nii.gz).
Is this dti.nii.gz for file I should use for correct conversion to reg.lta?
Thank you! M
On Wed, Nov 29, 2023 at 3:40 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Try to specify –src <> and –trg <> --src specify src image geometry (mov volume for TKREG/register.dat) --trg specify trg image geometry
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 Mirsol Choi Sent: Wednesday, November 29, 2023 5:32 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hi Yujing,
I really appreciate your quick response.
The following is the error I get when I try to perform this:
Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat --outreg reg.lta
7.4.1
--inreg: register.dat input TK REG transform.
--outreg: reg.lta output reg.dat matrix.
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
error: corRead(): can't open file /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info
ERROR readREG: cannot read src MRI
Mirsols-MacBook-Pro:dtrecon mirsolchoi$
Is there an additional file I need to complete this process?
Thank you so much for your time.
Mirsol
On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: You can try lta_convert.
Best,
Yujing
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 Mirsol Choi Sent: Wednesday, November 29, 2023 5:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hello there,
I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data.
I have tried to perform bbregister, but the alignment is completely off.
Thank you so much for your time! Mirsol _______________________________________________ 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/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rPNfZCqlx1FynjTqlfu6S34aqEatZuKRZs2wr1dsd3zdLiZfXiS--s-au26O8n4vYtdS6hTZXPRmbMwsKgPOUyBhzwRzfmpj2e504WULnnxGgg2aDR4zWxspSKN1E3FoVpyfnSr3vL_SJonRCVW-ENaJOrNlbAFTvjQ5VkSP3Wx_xCte0P8BNZT6d5mOtTFCF20ckxPDDWTPfvGIfXWvBIZnJ2HE8790vLymblOd5h7fRMDT8ZnEuBN5vEZscSF_RB1_xVNelSTyepz1mdP6dWClmntOFYOTkvfQtFdwxw/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/compliancelinehttps://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/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/compliancelinehttps://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Mirsol Choi