Can you be more specific about why it is not working? You definitely need to run bbregister to create a registration file
On 11/17/2021 7:09 AM, m-maiworm@web.de wrote:
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Dear List, I first run the recon-all stream using a MPRAGE as input, then bbregister to move other mri-sequences to this MPRAGE. Now I want to transfer the values from these mri-sequences to the surface, so that I can calculate on the surface and perform a group analysis. I tried different input files, but it doesn't work... my command is mri_vol2surf --src /path/to/my/subject --out /path/to/my/output --srcreg ???? --surfreg --hemi ?h --fwmh 1,5 I wonder wheather I need an extra step to perform the registration file? Because in my current freesurfer output I can't find an "registration.dat"... Moreover I want to create thalamus/basalganglia/ventricle/amygdala etc masks, and I don't know how to automate this - does anybody know if there exists a command? Thanks for your help! Best, M
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Try this bbregister --s subid --mov mcT2_MAP.nii.gz --reg T2.reg.lta --t2 Also remember to send terminal output and log file
On 11/17/2021 10:32 AM, m-maiworm@web.de wrote:
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Well, it gives out an error that the file given for srcreg is unkown or cannot be found. So mainly I think the problem is that I defined the "wrong" file there. I run bbregister with the following command: bbregister --s subid --mov mcT2_MAP.nii.gz --init-rr --reg T2.reg --t2 --o /path/to/my/output I also tried to use T2.reg, but I didn't work: "ERROR: Option T2.reg is unknown" *Gesendet:* Mittwoch, 17. November 2021 um 16:11 Uhr *Von:* "Douglas N. Greve" dgreve@MGH.HARVARD.EDU *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Using Mri_vol2surf Can you be more specific about why it is not working? You definitely need to run bbregister to create a registration file On 11/17/2021 7:09 AM, m-maiworm@web.de wrote:
External Email - Use Caution Dear List, I first run the recon-all stream using a MPRAGE as input, then bbregister to move other mri-sequences to this MPRAGE. Now I want to transfer the values from these mri-sequences to the surface, so that I can calculate on the surface and perform a group analysis. I tried different input files, but it doesn't work... my command is mri_vol2surf --src /path/to/my/subject --out /path/to/my/output --srcreg ???? --surfreg --hemi ?h --fwmh 1,5 I wonder wheather I need an extra step to perform the registration file? Because in my current freesurfer output I can't find an "registration.dat"... Moreover I want to create thalamus/basalganglia/ventricle/amygdala etc masks, and I don't know how to automate this - does anybody know if there exists a command? Thanks for your help! Best, M _______________________________________________ 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_______________________________________________ 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/1h8T1xiRBLY5YKXX9YWIaXJ8ThP3wdsTQKEqjP17-65PYKVzCzOEqf3qxitGPRa1U_XmkHXmblm4WKGyYzHfGaHgaIqbv8s0Y-gv-Rng1sZdrn7cuDvc3D-jZ50taKRGkpYx3RUXV3FHmxcy3_SIVxB8IZ1TbwggnZV9TjBlIFEDsyotVI0aF0cH8ZqysQ2xTc3FRvkwldo4P4XkSPk_B-AzO5t9n-KaKxYejRSzf8jiqZvStUOu7v62Bid4K0cbekgctnqYZrWpd1SNFRERAMMdoDX-gIXNv-jOHJYNPw7AHze2wRpLjLfuz_mB_WyXggqSXHS8qKG2XeMp4s4XUQQ/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* http://www.massgeneralbrigham.org/complianceline http://secure-web.cisco.com/15_8g_MKxi4xv6TegXuvosJTe00lQ-YxX-dEkvn2RJRMZaYHvP5dr-zLsTMdFzogJQFLJ2XjN0ufbkzVF3X-X_6KLdePYWIxyP4f2nMyP2euxZhUjSMHq4xsEDyvTzADAzaMBt_8j7rD_yWHAruYM0kMU6eNIdo3gEzVqUwurTkhPOk0cvL3Jbmj7I_7QkcFSpc8vRGAmDPXKrWlTC7-n-2nJNLRxG-jwLVmCOFRjrEXsFTy7_U80w_unjbV70oMmDZ4m2cRKCVVe6m36DjJcBldQnHvbMhrPwQxvjvxatMoXuOXIMuiHtOTWTF3GEZaLqTUpaAqTVgM1Bk5l1mvoaQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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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