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Thank you! That does describe the problem. I tested that out and it just completed and unfortunately that adjustment didn't change things significantly from the original run. A screenshot is attached. I made very very VERY sure that the recon-all log for the right side screenshot did really incorporate the xopts file, and that the WhitePreAparc call had that flag included correctly. The output on the right side of this screenshot is 100% definitely using the custom xopts file and in the recon-all.log it correctly added the --rip-bg-no-annot flag to WhitePreAparc. Any chance you have other suggestions in this vein? Happy to send these output subject directories if needed. Thanks again, Sarah ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, March 27, 2023 10:06 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3
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Does this describe the problem? https://secure-web.cisco.com/1T1FZK7qw7-Q0b7XZDB528AQkugcpuc-Lxb6NUVW0q_VAdO...https://secure-web.cisco.com/1l-IDmQ2XgFbr_hrqvkMaCbn3jZ7ogYL3PZ-zetLeQW1VkhgTXzNy6uFQMYmPSSa6WPiAj8iAzrqXNCrhhQztHqeGcwhlf8kMUYbByOivngTgYzBhmxZ7FMkiH9RwuSHPefwTJpwglephcndpB0BoIS12wvsviRt_wLPP1duX6dAh4qI1uAK5jptvKtPHxjXxMAiIh7NLdXI04R0ihioJpBU1KZEcRB4JY_LgnNQ-pAnyvXB1UlIrs4HcQL-pn-Dz3JMe285YK127i-L52ZPXJss11VorXBQuGv-dzoi2mG1-e0RuV8bZ0ePWIZs6V6vY3iryTMaaeEomnYQdgHXg8Q/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FReleaseNotes%26data%3D05%257C01%257Csarahkeefe%2540wustl.edu%257C6e0aa60ed1ca49477c1608db2ed4ecf0%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C638155264274677619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D8bsYLWFStlXfF8zaBF52GG%252F59T68ntmB%252B2yvF77sHXA%253D%26reserved%3D0 Bug fix: improve surface placement in inferior frontal area near putamen. There are some cases where the white surface is not placed well in these areas because of the close proximity of putamen to cortex; it is probably the case that the surface is not well-defined in this region anyway, but the placement can be improved by creating an expert options file with the line "WhitePreAparc --rip-bg-no-annot" Let me know if that fixes the problem
On 3/22/2023 5:00 PM, Keefe, Sarah wrote:
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Hi FreeSurfer Team,
Our group is working on reprocessing scans that we originally processed (performed quality control and edited where necessary) with FreeSurfer 5.3 with the HCP patch. We are aiming to reprocess everything with FreeSurfer version 7.3.2. So far when checking and editing FreeSurfer 7 outputs we're regularly seeing areas of brain that should be included within the white matter surface but are not, particularly in the accumbens and orbitofrontal areas. The areas are of lower intensity within the scans, but FreeSurfer 5.3 is able to handle these areas accurately - we don't see these issues in our runs on the same scan files done in FreeSurfer 5.3.
I've attached a screenshot of the Freesurfer output of each version side by side on one of the slices where the exclusion is happening. We're seeing this on maybe 1 in 10 Freesurfer 7 scans. All did fine in 5.3. We're finding that the problem is not limited to certain scanners - one of these examples is from a Biograph PETMR scan and the other is from a Prisma.
Is there a recommended flag or flags we could use with Freesurfer 7 recon-all that might get us closer to the way 5.3 handles this?
The Freesurfer 5.3 parameters we originally used were: -all -qcache -hippo-subfields -nocubic -mprage
The Freesurfer 7.3.2 parameters we are using now are: -all -qcache
I have the recon-all outputs of both versions and the original scan available and can send them via FTP if that would be helpful.
Other notes: Running with the -mprage flag added to the Freesurfer 7.3.2 recon-all launch was not different from the FS 7.3.2 recon-all launch without the flag but I can send that output along as well if it would be useful. Also, these examples are done in 7.3.2 but we've also run into this issue with 7.1.1.
Really appreciate any assistance you can provide, as trying to figure this out has been delaying our processing a bit. Thanks so much, Sarah
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