On 1/27/2021 1:34 PM, Nils B. wrote:
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Hello and thank you for you answer,
to the first point: Freesurfer is recognizing this area as Gray Matter. Can I just delete this part manually and see if the WM/GM pials are correct or would this lead to other problems?
You can do this. It is essentially a skull stripping error, though it is really hard to remove because it is between two bits of brain.
To the second point: I mean the tool, which enables me to do manual edits like deleting areas. It's the 4th tool from the left in the top bar of the Freesurfer GUI.
What editing did you do there? I don't think they look that unusual; sometimes you need to look in all 3 dims.
Best regards,
Nils
Am Mi., 27. Jan. 2021 um 00:41 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
On 1/26/2021 3:18 PM, Nils B. wrote:External Email - Use Caution Hello everyone, I'm analyzing 1,5T scans and I've two problems with the data quality of my participants, where I hope you can help me. 1. In two of my scans the participants have blurry areas near the cerebellum, which makes it nearly impossible for Freesurfer (Version 7.1) to set the pials correctly (see Appendix: Scan 1). Is this problem caused by movement while scanning or is there something i can do?This looks like it could be the transverse sinus vein and not brain tissue.2. Sometimes when I'm using the manual tool "recon-edit" for manual skullstrips the pials look weird after another recon (see Appendix: Scan 2, green box).I'm not sure what you did here. What is the "recon-edit" tool?I hope you can help me with this. Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.de <mailto:nils.tobias94@gmail.com> Web: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ <https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytxe9X-rKYktgU5BqHJRARTIIkVwUa0QcI5HtNkwNM92C4nHKmaQQc7fA6rMi17JoqvNzfMEGq_UrAXpLXHfNeA6rv-d_mBoaeR-dL3nY1MaBZK-yQjRhWv0RK2621oG_HGbXAN1wEBIMW2OQDWfLDv6H_CjwyyKTzKr4aE_8YaATJwviO5d9tdqlvcQMJDCW-gJ3ni4yh0zhsCI1GK9RgU-N0RMeK5Y9kWC-foM_vJA/https%3A%2F%2Fsug.uni-paderborn.de%2Fen%2Fsport%2Fsportpsychologie%2Fteam%2F> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://sug.uni-paderborn.de/department/it/ <https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytxe9X-rKYktgU5BqHJRARTIIkVwUa0QcI5HtNkwNM92C4nHKmaQQc7fA6rMi17JoqvNzfMEGq_UrAXpLXHfNeA6rv-d_mBoaeR-dL3nY1MaBZK-yQjRhWv0RK2621oG_HGbXAN1wEBIMW2OQDWfLDv6H_CjwyyKTzKr4aE_8YaATJwviO5d9tdqlvcQMJDCW-gJ3ni4yh0zhsCI1GK9RgU-N0RMeK5Y9kWC-foM_vJA/https%3A%2F%2Fsug.uni-paderborn.de%2Fen%2Fsport%2Fsportpsychologie%2Fteam%2F> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ebaicrtMvX86fCQuDMZFMWOkJ4vM6dRUCWNDuwB1kTnIAlWF7ricyaWny_TS9tByJ897UYA5_TGMwOmK95oibQxE8P80zyzBQFcuxlVEGJG820D8cuAS_3VespjTMVCQ-pTRbx9mRhlwWjYSlsr5WzlwzcA0wTq0zBZ13qPuX4kY-veBkEoLFaqa3d21DAF8IbaiwFiF3cl_EAfN8aPTVXT5e_psGThj24cWBUIPEpY6-6o5_CNWYRrouZEwaZ6y6xtZlyHsp-Gg7m7YrmXE_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ebaicrtMvX86fCQuDMZFMWOkJ4vM6dRUCWNDuwB1kTnIAlWF7ricyaWny_TS9tByJ897UYA5_TGMwOmK95oibQxE8P80zyzBQFcuxlVEGJG820D8cuAS_3VespjTMVCQ-pTRbx9mRhlwWjYSlsr5WzlwzcA0wTq0zBZ13qPuX4kY-veBkEoLFaqa3d21DAF8IbaiwFiF3cl_EAfN8aPTVXT5e_psGThj24cWBUIPEpY6-6o5_CNWYRrouZEwaZ6y6xtZlyHsp-Gg7m7YrmXE_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>--
Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401
Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.de mailto:nils.tobias94@gmail.com Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://secure-web.cisco.com/12L5BzXRxn0U_MtVCIYPpF_vPrWZBaleUFS-W6WNhqJUYQKOQoqm1tzVyl-4yrWZu7iwyy9BXFqtrO2xwdY1S_HsRrKNvdxqOm8-bHUb-1IeYDAi9y7GfJ2js9RBcLrHXrwdwatBxPsaBdDlOVWysOZiPEJ5tKw98YTHJdBAZHHyzwk1jOCJ8SmZt-pIQ1n109wWqpe8vOsbLM61xCv-qPVwVkC3H70UY1GtNFO9oSBmhlPJ4LFW_Jy9XSsi0KPl961WA1r6gUnk-ro9oLfvgkg/https%3A%2F%2Fsug.uni-paderborn.de%2Fen%2Fsport%2Fsportpsychologie%2Fteam%2F https://sug.uni-paderborn.de/department/it/ https://secure-web.cisco.com/12L5BzXRxn0U_MtVCIYPpF_vPrWZBaleUFS-W6WNhqJUYQKOQoqm1tzVyl-4yrWZu7iwyy9BXFqtrO2xwdY1S_HsRrKNvdxqOm8-bHUb-1IeYDAi9y7GfJ2js9RBcLrHXrwdwatBxPsaBdDlOVWysOZiPEJ5tKw98YTHJdBAZHHyzwk1jOCJ8SmZt-pIQ1n109wWqpe8vOsbLM61xCv-qPVwVkC3H70UY1GtNFO9oSBmhlPJ4LFW_Jy9XSsi0KPl961WA1r6gUnk-ro9oLfvgkg/https%3A%2F%2Fsug.uni-paderborn.de%2Fen%2Fsport%2Fsportpsychologie%2Fteam%2F
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve