[Freesurfer] Registration in PETSurfer

[Ruben Dörfel]

   External Email - Use Caution


Hi FreeSurfer Team,

I am currently using PETSurfer to analyze FDG data. Following the guide 
https://secure-web.cisco.com/11AP3L-fRQ1NyWLwYgy3qW-ObrGxWQsVDEGWJEidxYaLFleo8x6bV-bdH8eLZwLbRkWinVldOV1qDJy0v2d0UB8jW9t6WaSDIlGCVfwxhg2vbtB12Ci8gqdvbKFx-xKQxdJOqU-cL4kmTWApXkud2Iz_30imjhwVnRqTX2w7sgqflnsIyXNoWDrvLiibLRpvobvmYNOLnKzv9Yxa9tx3CjO4Q0ZhM9oSx7Had2L8N8WCHOMfH9csV5xIk4roG1R2rGvGvBIoXfq6TVWtX0oc3RwbtAzii9QQV0jnAa1c73Js-ALAS8HTzQe_BXdeXzQMmj4wdaASOcKWyJ9Jt5JkKGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer, it is suggested 
that you use _mri_coreg_ to register PET and MRI images. However, I was 
wondering whether _bbregister_ might not be the more appropriate tool to 
use, especially in a case like FDG, where we have a lot of uptake in the 
brain.


Best regards,

--
Ruben Dörfel, MSc
PhD Student

Center for Psychiatry Research
Karolinska Institutet

Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline 
 .
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. 

Re: [Freesurfer] Registration in PETSurfer

[Douglas N. Greve]

bbregister is more sensitive to the smoothing in the PET images. This 
can create a confound between atrophy and registration. bbregister 
should only be used on non-smoothed data.


On 5/1/2024 5:06 AM, Ruben Dörfel wrote:


External Email - Use Caution

Hi FreeSurfer Team,

I am currently using PETSurfer to analyze FDG data. Following the 
guide *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
, 
it is suggested that you use /mri_coreg/ to register PET and MRI 
images. However, I was wondering whether /bbregister/ might not be the 
more appropriate tool to use, especially in a case like FDG, where we 
have a lot of uptake in the brain.


Best regards,

--
Ruben Dörfel, MSc
PhD Student

Center for Psychiatry Research
Karolinska Institutet

Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline 
 .
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] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

External Email - Use Caution

Hello,

I wanted to bump this post once more to see if I can get any guidance here. I 
believe I am close to solving this problem, but I have two lingering questions 
that are preventing me from moving forward.

Thanks again.

Dan___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline 
 .
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. 

Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

[Krystal Xiwing Yau]

External Email - Use Caution

Dear FS experts,


I would like to follow up with the matter here - the T1.mgz isn't generated so 
I cannot inspect the image as instructed by the wiki page. I have checked the 
orientation on FreeView but it's correct. Would you please kindly advise?


Thank you so much. It's been grateful to have your guidance and support.


Sincerely,

Krystal


FreeSurfer Version: 7.3.2

OS: Linux on Ubuntu 23.04



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krystal Xiwing Yau 

Sent: 29 April 2024 16:58:18
To: Freesurfer support list
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error


External Email - Use Caution

Dear FS experts,


I am encountering an error when running recon-all. I followed the FAQ 

 page to rerun the command but still not running through. Would you please 
kindly advise? The log file is attached to this email.


Thank you.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline 
 .
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.