Hi Franchesca
It’s hard to say without seeing your data so we can diagnose what went wrong. If you upload a representative dataset we will take a look
Cheers Bruce
From: Franchesca Kuhney fkuhne2@uic.edu Sent: Wednesday, July 28, 2021 7:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfield Definition Errors
External Email - Use Caution Hi Juan and Bruce,
I wanted to follow up on my previous email. Do you have any recommendations to manually or automatically fix poor segmentations?
Thank you, Franchesca
Franchesca Kuhney, M.A. (she/her) Clinical Psychology Doctoral Student University of Illinois at Chicago Behavioral Sciences Building | Rm 3019 1007 W. Harrison St. | Chicago, IL 60607 [https://secure-web.cisco.com/1vGds0TwGsAb92XFFZpsY8Nsq5qYo_q35-h6HY0T8NxGmdd...] ----- Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. The information included in the email may be confidential and is meant only for the use of the intended recipient. If you received this communication in error, please notify the sender immediately and destroy the original information.
On Mon, Jul 19, 2021 at 9:54 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Definitely an ASEG problem that the subfield routine couldn’t recover from. Bruce: any ideas on what may have gone wrong? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.comhttps://secure-web.cisco.com/1bYlCIKFB4FFDxJqiNpu6c_O2e7ZSa71AKXm3I0iwjEN7hU8P35-hGUWzTZYfI8V6j_QVukKekgB7wKv3kPYI0GtdO2DCxdSw1qu8UBEMnmzAsQCw16LWfSk11LZE9hw8Da4aqqVnx1KMe-gxW-Mgi0dWhKnEfM2tM3J2bDrP0unXzYjoUgXEjcTMMNXzksh_9fSWHczHsMTn3r_Ha31vP-S0PExeYMxjLufFfPoPMejLSvAcYc6BJpR3UuVXBOPZ/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.jeiglesias.com%252F%26data%3D04%257C01%257Cfkuhne2%2540groute.uic.edu%257Cd02895bf36844b81462b08d94abcabb5%257Ce202cd477a564baa99e3e3b71a7c77dd%257C0%257C0%257C637622996476223787%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Djvuk3iny%252B%252BgGooICGRcU7TYwsZIQ82fRpyKJciOpdNg%253D%26reserved%3D0
On Jul 17, 2021, at 23:46, Franchesca Kuhney <fkuhne2@uic.edumailto:fkuhne2@uic.edu> wrote:
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I hope this is helpful, thank you!
Franchesca Kuhney, M.A. (she/her) Clinical Psychology Doctoral Student University of Illinois at Chicago Behavioral Sciences Building | Rm 3019 1007 W. Harrison St. | Chicago, IL 60607 [https://secure-web.cisco.com/1LKV93Gyim8oVzAYGWcdUGHuvXWUgTTt9QHoaHND-BtW2Z9...] ----- Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. The information included in the email may be confidential and is meant only for the use of the intended recipient. If you received this communication in error, please notify the sender immediately and destroy the original information.
On Tue, Jul 13, 2021 at 10:46 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Wow that is indeed terrible. Do you think you could send us the same sagittal slice for aseg.mgz, please? Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttps://secure-web.cisco.com/1Tr6swIzunZq8x06I1SUZ6Zcgx7DFFnRxlQgCp-WstnUnfkDHnFn_u0Ejy1bQY6Uht699WeVwcxjBaCaFySeGWP2mIdCwH3dq9f1i1aDtAb1gTS8I1Fwa9yPM-Pz2HtANJuwRRh0IJwJ-qwn4BUYpUBmko6pDlGXbA-Aa5qUdnOVNwf423dkz7h1feyo2yOTCkz_6s5Wi8R-y3gGhZVXj9jBeFDZORG8fOtOpkmvb72L1eJ-qCTA9R9ObD4K4-69j/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1c2BH1ZXpGZQe6RsWkBnoebiEpFJWKxz54CoSiUE-3J9UFMrYc70ztsR671EhXvjZpSUjirYplYd8Hvj4oJcaG2Q9A8E0KKy1w0DfWszhcXuY-P7j7OcFocCdSTvO_sdbJZWl9S5FbXzDWaZeAOJ-xX0gFXSzcfRFTPv1LisvRr5QPcSU-y2jpvz4eIDOuCcysVYzRGjXmDwnLp5jfs-Btor77GkXwXhCXSQSK1yyuUfxx3MkAZSenR_tJ9kns1wZ9SG4LJrdXZ9T0QwDr8ZoaQ%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.jeiglesias.com%2525252F%252526data%25253D04%2525257C01%2525257Cfkuhne2%25252540groute.uic.edu%2525257Cc0b17b2450f14bd2dba308d94679e4c2%2525257Ce202cd477a564baa99e3e3b71a7c77dd%2525257C0%2525257C0%2525257C637618311616679685%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DolNzm46i2ac3b5nKAde%2525252BM0prh4Daf6me38kEeA5bt%2525252B0%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cfkuhne2%2540groute.uic.edu%257Cd02895bf36844b81462b08d94abcabb5%257Ce202cd477a564baa99e3e3b71a7c77dd%257C0%257C0%257C637622996476223787%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DNB%252FENBz0psV7h81itypXQEnLBgdNtBfEaKo2kqSwK1s%253D%26reserved%3D0
On Jul 13, 2021, at 22:31, Franchesca Kuhney <fkuhne2@uic.edumailto:fkuhne2@uic.edu> wrote:
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Hi Juan,
So sorry for the delay. Attached is an example image. Thanks!
Best, Franchesca
Franchesca Kuhney, M.A. (she/her) Clinical Psychology Doctoral Student University of Illinois at Chicago Behavioral Sciences Building | Rm 3019 1007 W. Harrison St. | Chicago, IL 60607 [https://secure-web.cisco.com/1xumyEUYVfey7EOoL0PHtyPjSb43K_ZSoqzfAE-J9-kP-4H...] ----- Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. The information included in the email may be confidential and is meant only for the use of the intended recipient. If you received this communication in error, please notify the sender immediately and destroy the original information.
On Fri, Jul 9, 2021 at 1:49 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Franchesca, Could you please attach some images illustrating the problem? Cheers, /Eugenio
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On Jul 9, 2021, at 13:06, Franchesca Kuhney <fkuhne2@uic.edumailto:fkuhne2@uic.edu> wrote:
External Email - Use Caution
Hello,
I've run into an issue with the longitudinal hippocampus/amygdala segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized that a few subjects hippocampal segmentations were a poor fit. It appears that the segmentation includes their parahippocampal gyrus. I'm wondering if you have any recommendations for how to fix these either manually or automatically? Thank you!
Kindly, Franchesca
Franchesca Kuhney, M.A. (she/her) Clinical Psychology Doctoral Student University of Illinois at Chicago Behavioral Sciences Building | Rm 3019 1007 W. Harrison St. | Chicago, IL 60607 [https://secure-web.cisco.com/1puxmEK3mDm56IT5JV-3zOLSqMv5RYqFgYmoHYrQAp5MYBl...] ----- Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. The information included in the email may be confidential and is meant only for the use of the intended recipient. If you received this communication in error, please notify the sender immediately and destroy the original information. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1pWODTbP3rGHRWGvhM9exY_EAdqQVhY5u8pnnR0_0HvZ56MT-brRueKT6KItnQ8HYx7HGf9ualcI_F-G5HQsVMFfQbWaHwQ7_Q4xtoPuyaxqOy91usRhWT5lGuHl-uY1_lL8sPUxpTj5PWjFeqoXYRlrwuLY7YmR7TgtDOnXwivviIaLzCPdm054uQYdjSY_dtNRHPwTsJUQzh2WUZCUtwdu2Ya-17N13MsTkeR5xmqrAm3eL8CLWFwaP37OYOa6w/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1vio_JwzAp5_JU5pj97qlfqr095Xjir2d614dm5vdPjDnP3VmjXaA0yvWJuNHpDsody4nBEyB-8Cn935F16qI9Q1yDWPYc3vVDpYyK2M-yNjz02tG9jgO_Yv6q5tfaUnbJkSZ3dUf7Wk_DDImx_aY8MNgUdFXepBhgp0KH0Seqo_YwANigZPzJuFlO7QFrU6NqWTKUyTIJDQAKXUM5slQ8hbpU-4QE7YNOnT5gHOPeEpMyOdAracOMfCJOHdeeulUOMzt0itj9m8IrOLWVwh-xA%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1rM9wgo736dZL1oId0le05KfPQY7L7EgVOxbSrGLub9-vBq7SeeLk6hMYDo6-RMesE_UeAng94zT1-rSD6fdRW6ZrbkEnX8doeJcQOcAKkaGlyAZa4lCQCg2oA5VvpQ9ucdFJ4pzF7oC3sGaBTVPL0sexJnHWWBrZ-aymFdR6gXB69EaBwwLcxzmgg6eBDwoV45_2Flscmizi0VFWEjPNK1OPizS_jJtFHxBW9tVuw2Nq9VETIOV3j28i-noWZyN_o3Ogh0qhgXID6FxOKlUvUg%2525252Fhttps%252525253A%252525252F%252525252Fmail.nmr.mgh.harvard.edu%252525252Fmailman%252525252Flistinfo%252525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cfkuhne2%25252540groute.uic.edu%2525257Cc0b17b2450f14bd2dba308d94679e4c2%2525257Ce202cd477a564baa99e3e3b71a7c77dd%2525257C0%2525257C0%2525257C637618311616689644%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DeYcAdMN5mVmHsvo4IQ4NmEaOn7SKMVjCYOvUD5xScqk%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cfkuhne2%2540groute.uic.edu%257Cd02895bf36844b81462b08d94abcabb5%257Ce202cd477a564baa99e3e3b71a7c77dd%257C0%257C0%257C637622996476243695%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D55m9tL0%252B%252BFLtywba0mCKshSVwMCzFQzWIgv7luBFYNM%253D%26reserved%3D0
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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.massgen...https://secure-web.cisco.com/1Tran2oqhF2Dnc-TD9UianaP9rLCAPxu2hhAyRcvmX9ifpJ7p260ClNjBllOV7boPApcu0wZXeRyEyMbmiYtsGJB1lJjshMxvs7dtdQ5RaWW_ODgyGYg1LGicmL6e8MO4ejgzyJWM2JiTdmrdOz3g4BIfrIBu9nYARdeauqbeucRPU_HdLMsX-yaJep83LYKW8BZyJXdNZ3NxuBad3cO_vQ/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1G8y00lmpcIFq6LvZaZgAXhhSweFl1IJY8rScpb-x1S10JyGqGKbWhcuI_VkH5lZZ0LkYYgFv_tLMMvoulRC2oPpDAEZ3sU5RIMo9S0sNABOnhB11kcycdxekUzKXE38HqshZYYwr3P0a_3Nql4jy7xzGeTN0a0BZq5Rzc-HWtfo1xxr9SwvsfXzOuY02mQ0KK82VF_cyXwMOALwYREcJ2fT6zfzqAuZQteSrdS78it8Epyw35RmrzNMaNRtiNl8d0NO7uO8KFEo5GnnqJtz9Gg%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1fu-sqs22TdPMe3ksAY5BOqghxQl6_swvvAHO0OkF4fkD7WqfyAhpJfLD-AZwpGb31Wj6QY44pRWJR0XRVO-CN7oQieucdWFjwAJVJM5hRcUNMihRVnw641Uvrp8pMNZTQrhnC6lE1GMUAEzSJjeuuWGrkaovqNmcWjZTrVf1UjY8UprB7KR3Pwp_6bvYIuGXwyw8du4q_hKqHUhHUskf0Mnravn-0thICTwkfCXfazx3j07PDQZrNpZSC9V9pT1k9QIpmByuqrbaDZRoU0nP7A%2525252Fhttps%252525253A%252525252F%252525252Fnam04.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttp%25252525253A%25252525252F%25252525252Fwww.massgeneralbrigham.org%25252525252Fcomplianceline%2525252526amp%252525253Bdata%252525253D04%25252525257C01%25252525257Cfkuhne2%252525252540groute.uic.edu%25252525257C3086a2b623d64332e6cd08d9430a08f9%25252525257Ce202cd477a564baa99e3e3b71a7c77dd%25252525257C0%25252525257C0%25252525257C637614533646585052%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C2000%2525252526amp%252525253Bsdata%252525253DAF50RJgHCti6Cs7u3p6xtYFiTMEHU8WjwBILCWH5hxg%25252525253D%2525252526amp%252525253Breserved%252525253D0%252526data%25253D04%2525257C01%2525257Cfkuhne2%25252540groute.uic.edu%2525257Cc0b17b2450f14bd2dba308d94679e4c2%2525257Ce202cd477a564baa99e3e3b71a7c77dd%2525257C0%2525257C0%2525257C637618311616699597%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2lu . 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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. <Screen Shot 2021-07-13 at 3.50.59 PM.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1oo-o7d_nMqGq695_SiRe-a5etKEbK8f5dfi2KdC6Hdba9kstEZBqoS0-4_BeqW0gRbIoeEMFhdimB0y_Az2M8SkExghSVebCqj4ThlebJ5vlrVnbQHVjuHkmTEt3IFlW_IUyzrAligP_pCGMG9WRRwXf09ak2osaOIrUL9tJopTUb4rh54U0wvqajX6_uFZJM2P43T09Hm9HqfGd2vP1oSizBntmMPxyFhXNdUNy4Ncch1blepunJ0FhEm2WgoCO/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11yDxfSnqI2KldcrkVYsXvHyQqCYFoViiqs5m9vEUu88xj4ggDESl3UWJ__X6nI0ZsiAdo5XJg9tiKKMtuw8gXDGofpBx2eDhCQq0pkjq85Qt20CEbgVyz-bnm6BSO6mKvGFv-VEoj-XhlJUr7MhN-nixHYnNCqltNWZ3aPxkyOk8yq9jGf8HB0QbQUQPKeQsiPN0bxQ74YIwZJJcDbeVYnOxMR0Q6A1hpSIiqMk2jFiuWHfyV-FHYAV8noKLSKiaUF9DExbo4CQeT1wy6Jl6Xg%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cfkuhne2%25252540groute.uic.edu%2525257Cc0b17b2450f14bd2dba308d94679e4c2%2525257Ce202cd477a564baa99e3e3b71a7c77dd%2525257C0%2525257C0%2525257C637618311616709555%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253D5jgRbdQUMZFeHTTCePmGD1XDXrDIkLjxz0%2525252FuNQTKfKQ%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cfkuhne2%2540groute.uic.edu%257Cd02895bf36844b81462b08d94abcabb5%257Ce202cd477a564baa99e3e3b71a7c77dd%257C0%257C0%257C637622996476263606%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D5OCR8Sw0jbhOryn4jrlx17d5YWqiP6m3lZoz9GbR1mc%253D%26reserved%3D0
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