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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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Does this describe the problem? https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 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:
External Email - Use Caution
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
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use Caution
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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/196jaPodWXIbkrxBznUP_VeI-ZNbofTWu7dUl_gomoPSf0Q...https://secure-web.cisco.com/1aZLPk8I54TnrtsEDa9DfjuK-p9k-CGuHxZeyYXptL5gLs0fByGkfNSpB1iBmS0no_SGYtMZ8CQzmTHlPSuW5j1324X3KuaJ7n3nyVsOAIkkCupIij6JxzduU2BMiD8_lRQM1agLCeEa_Q0RvRPuhaX5qBR7sAhwFaNQcQP0rGMHqNZsBcDdD4Eo3KLjg4hT-yHc40PYkVGfBX3maLlX9gIr89QOk0nlaXZvoJcy8ky-6vTF-w3GlpQyMxtKM9f-ds_hLXIaNPsBY3Er_v0DY-cPvE9IaWP_ukfXryyYDalUceJAwNCL731qHKrWfRCVVjUCoqZYiiL8GDT5zYW1IPw/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D05%257C01%257Csarahkeefe%2540wustl.edu%257C6e0aa60ed1ca49477c1608db2ed4ecf0%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C638155264274677619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DAsdBFd%252FWIEi%252B3vOudKifF9aoMesUvRGrDtt8RKXu7z4%253D%26reserved%3D0
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-all -s subject -autorecon-pial ( this will do white and pial)
On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
External Email - Use Caution
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? *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 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:
External Email - Use Caution
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
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1aZLPk8I54TnrtsEDa9DfjuK-p9k-CGuHxZeyYXptL5gLs0fByGkfNSpB1iBmS0no_SGYtMZ8CQzmTHlPSuW5j1324X3KuaJ7n3nyVsOAIkkCupIij6JxzduU2BMiD8_lRQM1agLCeEa_Q0RvRPuhaX5qBR7sAhwFaNQcQP0rGMHqNZsBcDdD4Eo3KLjg4hT-yHc40PYkVGfBX3maLlX9gIr89QOk0nlaXZvoJcy8ky-6vTF-w3GlpQyMxtKM9f-ds_hLXIaNPsBY3Er_v0DY-cPvE9IaWP_ukfXryyYDalUceJAwNCL731qHKrWfRCVVjUCoqZYiiL8GDT5zYW1IPw/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D05%257C01%257Csarahkeefe%2540wustl.edu%257C6e0aa60ed1ca49477c1608db2ed4ecf0%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C638155264274677619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DAsdBFd%252FWIEi%252B3vOudKifF9aoMesUvRGrDtt8RKXu7z4%253D%26reserved%3D0
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
Understood, but it is strange that we are seeing this only in the rh. In 25 sessions (albeit a third fairly minor). We are less concerned about thickness in this region than impact on subcortical volumes.
We realize this probably can’t be fixed, but we wanted you to be aware of it.
Thanks,
Donna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Wednesday, March 29, 2023 at 8:58 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 * External Email - Caution * Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-all -s subject -autorecon-pial ( this will do white and pial) On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, March 27, 2023 10:06 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3
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External Email - Use Caution 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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oh, it won't have any impact on the subcortical volumes. Those are measured without reference to the surface. Or are you seeing something that looks funny? Look at the subcorts in aseg.mgz.
On 3/31/2023 8:22 AM, Dierker, Donna wrote:
External Email - Use Caution
Hi Doug,
Understood, but it is strange that we are seeing this only in the rh.
In 25 sessions (albeit a third fairly minor).
We are less concerned about thickness in this region than impact on subcortical volumes.
We realize this probably can’t be fixed, but we wanted you to be aware of it.
Thanks,
Donna
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Wednesday, March 29, 2023 at 8:58 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
** External Email - Caution **
Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-all -s subject -autorecon-pial ( this will do white and pial)
On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
* External Email - Use Caution * 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> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Monday, March 27, 2023 10:06 AM *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3 ** External Email - Caution ** Does this describe the problem? *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes <https://secure-web.cisco.com/1hQZSkMCAubCpiOS1Nk-bMXFhFBAOwATCh5TQaMNQ-qzYtNrQbRH1jfWi5XAUiYbYxx9NHn-mYsC3bnQdz2u0EhHEQxQxnXGjSis2kgIQp0N_3ovgqdEK_PDQMIsOrflqt04ilRecrSJSzn_eDA4h_jSTTwf0RCvu2dPHYzfa3UUxW9ZH-DTB0-Yrgt3IiZzscdePCREyAl00mfFc_27Nxyrpfo0ZYqr3wNFXiAKulSAhcWES3LJzRDet_Z037lORiHQ-xNgqkJvvDx0Uxz9ZQmz0fjwO9DPQhWfBUCv0Pc_dE-gosHXOqkz6Z04uICc38x8G-UTzZZUtYuvh5QPPhQ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1l-IDmQ2XgFbr_hrqvkMaCbn3jZ7ogYL3PZ-zetLeQW1VkhgTXzNy6uFQMYmPSSa6WPiAj8iAzrqXNCrhhQztHqeGcwhlf8kMUYbByOivngTgYzBhmxZ7FMkiH9RwuSHPefwTJpwglephcndpB0BoIS12wvsviRt_wLPP1duX6dAh4qI1uAK5jptvKtPHxjXxMAiIh7NLdXI04R0ihioJpBU1KZEcRB4JY_LgnNQ-pAnyvXB1UlIrs4HcQL-pn-Dz3JMe285YK127i-L52ZPXJss11VorXBQuGv-dzoi2mG1-e0RuV8bZ0ePWIZs6V6vY3iryTMaaeEomnYQdgHXg8Q%252Fhttps%25253A%25252F%25252Fnam10.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsurfer.nmr.mgh.harvard.edu%2525252Ffswiki%2525252FReleaseNotes%252526data%25253D05%2525257C01%2525257Csarahkeefe%25252540wustl.edu%2525257C6e0aa60ed1ca49477c1608db2ed4ecf0%2525257C4ccca3b571cd4e6d974b4d9beb96c6d6%2525257C0%2525257C0%2525257C638155264274677619%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253D8bsYLWFStlXfF8zaBF52GG%2525252F59T68ntmB%2525252B2yvF77sHXA%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cdonna%2540wustl.edu%257Cdf85cff1a9c8423aa2cc08db305db62a%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C638156951270140107%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DWvaAlFKEq76ZJGr1q%252BBXtw%252F3VYBaz2qAzCtR5mB9dk0%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: * External Email - Use Caution * 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 ------------------------------------------------------------------------ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It's definitely affecting segmentation in the aseg.mgz, as well as the aparc+aseg.mgz which is what we usually use. Screenshots attached (FreeSurfer 7.3.2, "-all -qcache", no editing performed yet). It's over-labelling orbitofrontal here which we see a lot with these. We also see it affecting insula, accumbens, and putamen labeling. I wouldn't be concerned if it wasn't so biased toward the right hemisphere every time. We haven't seen it happen on the left yet.
The 255 voxels on brain.finalsurfs.manedit.mgz helped things somewhat but at this point the 5.3 results with no edits are still looking consistently better in this area. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, March 31, 2023 8:43 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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oh, it won't have any impact on the subcortical volumes. Those are measured without reference to the surface. Or are you seeing something that looks funny? Look at the subcorts in aseg.mgz.
On 3/31/2023 8:22 AM, Dierker, Donna wrote:
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Hi Doug,
Understood, but it is strange that we are seeing this only in the rh.
In 25 sessions (albeit a third fairly minor).
We are less concerned about thickness in this region than impact on subcortical volumes.
We realize this probably can’t be fixed, but we wanted you to be aware of it.
Thanks,
Donna
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Wednesday, March 29, 2023 at 8:58 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3
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Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-all -s subject -autorecon-pial ( this will do white and pial)
On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, March 27, 2023 10:06 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3
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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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right, but it is not affecting the subcortical structures (eg, compare to aseg.presurf.mgz)
On 3/31/2023 1:14 PM, Keefe, Sarah wrote:
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It's definitely affecting segmentation in the aseg.mgz, as well as the aparc+aseg.mgz which is what we usually use. Screenshots attached (FreeSurfer 7.3.2, "-all -qcache", no editing performed yet). It's over-labelling orbitofrontal here which we see a lot with these. We also see it affecting insula, accumbens, and putamen labeling. I wouldn't be concerned if it wasn't so biased toward the right hemisphere every time. We haven't seen it happen on the left yet.
The 255 voxels on brain.finalsurfs.manedit.mgz helped things somewhat but at this point the 5.3 results with no edits are still looking consistently better in this area.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Friday, March 31, 2023 8:43 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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oh, it won't have any impact on the subcortical volumes. Those are measured without reference to the surface. Or are you seeing something that looks funny? Look at the subcorts in aseg.mgz.
On 3/31/2023 8:22 AM, Dierker, Donna wrote:
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Hi Doug,
Understood, but it is strange that we are seeing this only in the rh.
In 25 sessions (albeit a third fairly minor).
We are less concerned about thickness in this region than impact on subcortical volumes.
We realize this probably can’t be fixed, but we wanted you to be aware of it.
Thanks,
Donna
*From: *freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Date: *Wednesday, March 29, 2023 at 8:58 AM *To: *freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3
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Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-all -s subject -autorecon-pial ( this will do white and pial)
On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
* External Email - Use Caution * 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 <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Monday, March 27, 2023 10:06 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3 ** External Email - Caution ** Does this describe the problem? *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes <https://secure-web.cisco.com/173dn3YRA91CeZNjr41unADI_lyEjzse5mbYKaXUefAsvapNx3bBZzAwl1rFsCztjyiL-kPIIIWN_fSMOngrAC9fV3fu7YK0LQM8J3Z3Rz3NEk5IRpABR-EyWAA49e5pGqbEAF0DiGjJC2Rlov_IxoMySVdKD2i8EIwFDpPo2d7karK-gneusiOKZ7m46oDEb33yreeRK4A47bTaSG1ybcL9HLV7fhyulzJRsChkKw02AK1kUbT-OZyMC13yoiFYD1hjUND4qBP5gg_PHV7RaJQ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1hQZSkMCAubCpiOS1Nk-bMXFhFBAOwATCh5TQaMNQ-qzYtNrQbRH1jfWi5XAUiYbYxx9NHn-mYsC3bnQdz2u0EhHEQxQxnXGjSis2kgIQp0N_3ovgqdEK_PDQMIsOrflqt04ilRecrSJSzn_eDA4h_jSTTwf0RCvu2dPHYzfa3UUxW9ZH-DTB0-Yrgt3IiZzscdePCREyAl00mfFc_27Nxyrpfo0ZYqr3wNFXiAKulSAhcWES3LJzRDet_Z037lORiHQ-xNgqkJvvDx0Uxz9ZQmz0fjwO9DPQhWfBUCv0Pc_dE-gosHXOqkz6Z04uICc38x8G-UTzZZUtYuvh5QPPhQ%252Fhttps%25253A%25252F%25252Fnam10.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1l-IDmQ2XgFbr_hrqvkMaCbn3jZ7ogYL3PZ-zetLeQW1VkhgTXzNy6uFQMYmPSSa6WPiAj8iAzrqXNCrhhQztHqeGcwhlf8kMUYbByOivngTgYzBhmxZ7FMkiH9RwuSHPefwTJpwglephcndpB0BoIS12wvsviRt_wLPP1duX6dAh4qI1uAK5jptvKtPHxjXxMAiIh7NLdXI04R0ihioJpBU1KZEcRB4JY_LgnNQ-pAnyvXB1UlIrs4HcQL-pn-Dz3JMe285YK127i-L52ZPXJss11VorXBQuGv-dzoi2mG1-e0RuV8bZ0ePWIZs6V6vY3iryTMaaeEomnYQdgHXg8Q%2525252Fhttps%252525253A%252525252F%252525252Fnam10.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fsurfer.nmr.mgh.harvard.edu%25252525252Ffswiki%25252525252FReleaseNotes%2525252526data%252525253D05%25252525257C01%25252525257Csarahkeefe%252525252540wustl.edu%25252525257C6e0aa60ed1ca49477c1608db2ed4ecf0%25252525257C4ccca3b571cd4e6d974b4d9beb96c6d6%25252525257C0%25252525257C0%25252525257C638155264274677619%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C3000%25252525257C%25252525257C%25252525257C%2525252526sdata%252525253D8bsYLWFStlXfF8zaBF52GG%25252525252F59T68ntmB%25252525252B2yvF77sHXA%25252525253D%2525252526reserved%252525253D0%252526data%25253D05%2525257C01%2525257Cdonna%25252540wustl.edu%2525257Cdf85cff1a9c8423aa2cc08db305db62a%2525257C4ccca3b571cd4e6d974b4d9beb96c6d6%2525257C0%2525257C0%2525257C638156951270140107%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DWvaAlFKEq76ZJGr1q%2525252BBXtw%2525252F3VYBaz2qAzCtR5mB9dk0%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Csarahkeefe%2540wustl.edu%257C95d8e4cd0383459af58608db31ee0420%257C4ccca3b571cd4e6d974b4d9beb96c6d6%257C0%257C0%257C638158670566704203%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DM3413qVRQ8XLATVuHfNFBaGEzhRtcrxegDbWegMfLWQ%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: * External Email - Use Caution * 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 ------------------------------------------------------------------------ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Dierker, Donna -
Douglas N. Greve -
Keefe, Sarah