[Freesurfer] Multi-echo FLASH
Hi all, I'm building a scan protocol for what is primarily a MEG study, which needs T1 information for co-registration and T1/T2 information to construct an accurate BEM from the inner skull surface. It seems like the two multi-echo FLASH sequences at 5 and 30 degrees would give me all of the information that I need without an MPRAGE, but I'm not sure how well the two MEFs work in the standard Freesurfer pipeline. Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5 and 30 degrees, combine them following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF, and send the resulting T1 to recon-all? With my scan time constraints, the alternative would be to acquire a multi-echo MPRAGE and a single 5-degree MEF. Thanks for any help on what is probably a naïve question. Jon Houck ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Multi-echo FLASH
Hi Bruce, Great, that will simplify things considerably. Thank you for the info. Jon On Fri, Apr 25, 2014 at 9:35 PM, Bruce Fischl wrote: > Hi Jon > > yes, that works fine. The mprage gives better CNR/unit time in the cortex, > but if you are really only interested in MEG that is probably a secondary > concern (it would be important if you were doing e.g. a thickness study) > > cheers > Bruce > > On Fri, 25 Apr 2014, Jon Houck wrote: > > Hi all, >> >> I'm building a scan protocol for what is primarily a MEG study, which >> needs T1 information for >> co-registration and T1/T2 information to construct an accurate BEM from >> the inner skull surface. It >> seems like the two multi-echo FLASH sequences at 5 and 30 degrees would >> give me all of the information >> that I need without an MPRAGE, but I'm not sure how well the two MEFs >> work in the standard Freesurfer >> pipeline. >> >> Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5 >> and 30 degrees, combine them >> following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF, >> and send the resulting T1 to >> recon-all? With my scan time constraints, the alternative would be to >> acquire a multi-echo MPRAGE and >> a single 5-degree MEF. >> >> Thanks for any help on what is probably a naïve question. >> >> Jon Houck >> >> >> > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz is missing mri_make_bem_surfaces binary
External Email - Use Caution Hi, It looks like the ubuntu 18 download for freesurfer 7.3.2 (freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275) doesn't have the binary for mri_make_bem_surfaces. The file in this version is a bash script that prints the message "error: mri_make_bem_surfaces has been removed from this version of freesurfer. For further information, please post to the help list at freesurfer@nmr.mgh.harvard.edu". The file isn't listed in 'attic' anymore on github, but for ubuntu 18 seems to be handled as if it was. The tarballs for the other 4 linux distributions are fine and only the ubuntu 18 tarball and .deb have this issue. Is this intentional? I didn't see anything in the release notes -- apologies if I missed something there. Thanks Jon Houck ___ 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.
Re: [Freesurfer] freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz is missing mri_make_bem_surfaces binary
External Email - Use Caution That makes sense, thanks for the explanation. Yes, MNE & MNE-python still rely on the command, which was how I noticed the issue. Best Jon On Wed, Aug 17, 2022 at 7:13 PM fsbuild wrote: > > Hello John, > > The mri_make_bem_surfaces command had been put in the attic and removed > from all platform builds, but was added back for some OS’s used by a > different imaging project back in 2020. It was not restored for CentOS6 > and Ubuntu18 builds.I don’t think that command has been > updated/supported since ~2001. We have discontinued CentOS6 builds and I > suspect Ubuntu18 will be next since Ubuntu18 LTS (long term stable release) > expires in Q1 2023 since both Ubuntu 20 and Ubuntu 22 now have LTS releases. > > - R. > > On Aug 17, 2022, at 15:07, Jon Houck wrote: > > External Email - Use Caution > > Hi, > > It looks like the ubuntu 18 download for freesurfer 7.3.2 > (freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275) doesn't have the > binary for mri_make_bem_surfaces. The file in this version is a bash > script that prints the message "error: mri_make_bem_surfaces has been > removed from this version of freesurfer. For further information, please > post to the help list at freesurfer@nmr.mgh.harvard.edu". > > The file isn't listed in 'attic' anymore on github, but for ubuntu 18 > seems to be handled as if it was. The tarballs for the other 4 linux > distributions are fine and only the ubuntu 18 tarball and .deb have this > issue. Is this intentional? I didn't see anything in the release notes -- > apologies if I missed something there.. > > Thanks > > Jon Houck > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1-FrN79O0GRm9lZO9kL_q4Esdt2Fjc35_eRWkTlgNzIbe07AoFpDlw5Tj0lDbYUKRTy2vS4YYugti0f2COcuBjMPtt-GCLjwJtTlTXBn8jUxBu0vMOTMHVga5FJ1UfxXOdadaksDelySgsRtHS9pVS2_W6c8AXPZbiQrzN0GSree7SOlv9leo1z-HHImwgzj-vW-S5uu_tASLwc2R7FqPZSw-V6KgQlHK5Uk-9hZTbYfx1bwWUI-faB20dz5l60j9wr_nIfmoFz1XzES8UN5-vfmEuYVCblDOWr5AiRcwoDJVYNBWM0d23Ge83Dm5TPX5jHpGa1nICfFtPNwQw9MgRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > ___ 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.
