External Email - Use Caution
Dear developers,
Did you have time to look at the problem with flairpial flag?
Thank you
Silvia
From: "Silvia De Francesco" <sdefrance...@fatebenefratelli.eu>
To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 29, 2023 5:42:43 PM
Subject: [Freesurfer] FLAIRpial bug
External Email - Use Caution
Dear developers,
We encountered the bug related to the analysis with FLAIR in recon-all
(recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We
obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v.
7.3.2
We also tried to run the analysis placing the line PlaceMMPialSurf
--mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50
in the global-expert-options.txt file in the $SUBJECTS_DIR and run recon-all -s
${subj} -FLAIRpial -autorecon3, the output seems better but the pial is ever
worst than with only T1.
What does the values of mm_min_inside mm_max_inside mm_min_outside
mm_max_outside mean?
Some suggestions to solve this problem?
Thank you
Silvia
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/13q_qAD4DXzKJ8xfCk3WJc0XMMrQwxADmA3xBWdixEXzmaxPZsiFVIPNLm-N0GZeDTagqhJcRYE4f5mNKkAFI2HQe8iX1bF_54TZMiEH0fLFj6qP8Bi0sCGW4jpRa5vCR66omnODUJjYImCbd-x5V-Dp1MrepYP9Do4v_3ZbU05fX1TCEwUzyap87jEXDof2WpZR4GlfyXXPStq183potIUpdia0cQflPJyhvh7ShJSCgRVgieQq-0pfuQcvmKWUY-ahJg0VAtyG2E-SpnLAQVp4r-ob7LCTfeadYaZkAxc-uJ4BW1Dc7e1V31OD-QlWD/https%3A%2F%2Furlsand.esvalabs.com%2F%3Fu%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26e%3D76da4eeb%26h%3D75bef3c1%26f%3Dy%26p%3Dn
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/1ONHQ9jYlyzxqPlWo6a_ZsJ4weQbSVEbVakdm7HSqQVGkjTsJOacHztfIBE3H8nVm6sjwIj0klXkOT0EFoEpjFlswjXxfZvRHtdPvrBDifCLzmMXTW6jJkhIaRM6Mxq1DnyyRrgvEHNoy7jb-Yz5bhPXFN9Y2iIUjqINlotPW21lj5IwnVEvdZ3N0FYNJlWXxcKLwfKwCmWWl6zkF0e23kvdMR7S4Bb3jHVaGUAUUBJqoWJkDljS-lTBNxSVzo3z5whEHgSDuiM7uOehw8sABW_2KDMO5qN74NkNG9-PPJAaFJbcdkM1C6yUosWQSV0UB/https%3A%2F%2Furlsand.esvalabs.com%2F%3Fu%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26e%3D76da4eeb%26h%3Df52a8379%26f%3Dy%26p%3Dn
<
https://secure-web.cisco.com/1ONHQ9jYlyzxqPlWo6a_ZsJ4weQbSVEbVakdm7HSqQVGkjTsJOacHztfIBE3H8nVm6sjwIj0klXkOT0EFoEpjFlswjXxfZvRHtdPvrBDifCLzmMXTW6jJkhIaRM6Mxq1DnyyRrgvEHNoy7jb-Yz5bhPXFN9Y2iIUjqINlotPW21lj5IwnVEvdZ3N0FYNJlWXxcKLwfKwCmWWl6zkF0e23kvdMR7S4Bb3jHVaGUAUUBJqoWJkDljS-lTBNxSVzo3z5whEHgSDuiM7uOehw8sABW_2KDMO5qN74NkNG9-PPJAaFJbcdkM1C6yUosWQSV0UB/https%3A%2F%2Furlsand.esvalabs.com%2F%3Fu%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26e%3D76da4eeb%26h%3Df52a8379%26f%3Dy%26p%3Dn
> .
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://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.
