I recently found a bug in the pial placement refinement with FLAIR images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug caused the pial surfaces to not extend nearly far enough. It has been fixed in the development version of FS and so will be in future versions. If you want to access the fix before then, create a $SUBJECTS_DIR/global-expert-options.txt with this line
PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50
sorry for any inconvenience doug
External Email - Use Caution
Thanks for the update!
If I recall it correctly, in our lab we did notice that to be an issue with T2 images (v7.1.1) as well (recon-all -T2).
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
On Dec 15, 2022, at 11:46 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
[CAUTION: Non-UBC Email]
I recently found a bug in the pial placement refinement with FLAIR images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug caused the pial surfaces to not extend nearly far enough. It has been fixed in the development version of FS and so will be in future versions. If you want to access the fix before then, create a $SUBJECTS_DIR/global-expert-options.txt with this line
PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50
sorry for any inconvenience doug
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VBaX-q4rOOKL46SYAdzbjRqy1TECu4XZl9lxlg_d5rC1jY... 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/1pg8KtII3OPnSeFwA0GPvJcYs0xEOFxZ8JinC3_bYl6sDGS... https://secure-web.cisco.com/1pg8KtII3OPnSeFwA0GPvJcYs0xEOFxZ8JinC3_bYl6sDGSvQToGI2pMzH3u3JFtbr1TcvE2fzx1WFxuFXbnvIgmORnI3defj_ZxNQ-LfRwc5KW6PERiDqK1u5ldBDahZiG2nNoFIpD0xQ6EQF_vIdtrozR6SYBbcnZIsdHB5QoETq8qEUP3lOqmNLnvC6sQF_zyX8gyBWkkejWrybADBaosc2I6QnUNE7WMjPq0qoDZ27iCqokPLBcZHSwfj3dessSvolTGEMF6BWG_6I4Y8gHJV5hRHwAFCUtLYpUh_oHdxsNCMwtFyeMayYHX7vo4w42j5isZJ-pwQe-hGqJzfUQ/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.
Right, it only affects FLAIR, not T2
On 12/15/2022 4:51 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Thanks for the update!
If I recall it correctly, in our lab we did notice that to be an issue with T2 images (v7.1.1) as well (recon-all -T2).
Nárlon Cássio
*Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
On Dec 15, 2022, at 11:46 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
[CAUTION: Non-UBC Email]
I recently found a bug in the pial placement refinement with FLAIR images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug caused the pial surfaces to not extend nearly far enough. It has been fixed in the development version of FS and so will be in future versions. If you want to access the fix before then, create a $SUBJECTS_DIR/global-expert-options.txt with this line
PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50
sorry for any inconvenience doug
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 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.
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Douglas N. Greve