There is an automatic topology fixer in the stream. While sometimes it
fixes an topo error properly, it does not always do so, so you will need
to see whether it has fixed is or not. It is the white surface that is
in error, which is created from the wm.mgz (or filled.mgz), so you will
need to fix one of those volumes.
On 12/14/2021 5:26 AM, Nilab Nasrullah wrote:
External Email - Use Caution
I am using freesurfer 7.1.This particular subject's segmentation
didn't include the cerebral cortex of the occipital lobe (see image
1). Although I can see there are defects in that specific place, there
are also defects in other places (see atttached images). I have
followed the instructions on how to correct topological errors but
that doesn't seem to help much since it is the grey matter that is not
included in the segmentation.
Can you provide me with some instructions on how to fix these defects?
Thanks,
Nilab
------------------------------------------------------------------------
*From:* Douglas N. Greve <[email protected]>
*Sent:* 11 December 2021 00:24
*To:* Nilab Nasrullah <[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [Freesurfer] Help
The data look pretty noisy in those images. My guess is that the WM is
not getting segmented properly in that temporal area or there is an
incorrectly fixed topology error. Try looking at the wm.mgz (or the
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz
to see where the defects are.
On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:
External Email - Use Caution
Sure. See attached.
//Nilab
------------------------------------------------------------------------
*From:* Douglas N. Greve <[email protected]>
<mailto:[email protected]>
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah <[email protected]>
<mailto:[email protected]>; [email protected]
<mailto:[email protected]>
<[email protected]> <mailto:[email protected]>
*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?
On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:
External Email - Use Caution
I am attaching a few screenshots of the segmented brain as
zip-files. Hopefully, you can see the results. If not, let me know
so I can send it to you in a different format.
Thanks,
Nilab
------------------------------------------------------------------------
*From:* [email protected]
<mailto:[email protected]>
<[email protected]>
<mailto:[email protected]> on behalf of Douglas
N. Greve <[email protected]> <mailto:[email protected]>
*Sent:* 29 November 2021 04:01
*To:* [email protected]
<mailto:[email protected]>
<[email protected]> <mailto:[email protected]>
*Subject:* Re: [Freesurfer] Help
Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
External Email - Use Caution
Hi,
I am editing subjects for a research project. After reconstruction,
some parts of the brain are not included in the segmentation.
Often, some parts of the temporal lobe and the cortex of the
occipital lobe are not included. In some cases, the cortex of the
frontal lobe is also affected.
I have tried using controls points, but the results don't change. I
have also reconstructed them again, running autorecon1 and
autorecon2&3 separately. I have lowered the watershed parameters,
used the gcut command and edited manually after autorecon1 but in
the end, the results don't vary significantly compared to running
recon-all -all.
What can I do to include the missing parts?
Thanks,
Nilab
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/Sending email to Karolinska Institutet (KI) will result in KI
processing your personal data./ You can read more about KI’s
processing of personal data here
<https://secure-web.cisco.com/1R6PMKd7mU2_MHhIWz8mPfsS7neJAGdLDDbjihjjxqgHA1kDZpfs8xW9A2Q8WnZIN4eRQhjG0Cx9pB3BgBwp7_zk31qP2j6KkEtxQov6MOYmeCQ1YaRju3v8uAAhIDJUuVvbSE1Ih01gWAeJAliI6OaMTJjD6e7sDsJp9C1Q0MuIr_3fWBP7ISWSiUdZWx_xwl-ZsnmQlTXBIZy32uTIBqOai-UAZ4jZOTj8u8HhMNJb8fEPGLkdX4RqUEgRL1tq9cHbHOTBLch75dQdGKo_jcw/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1lmFcjGGYhT8Lb-8v-jAcUDrxjoMyBBbd5y2oyla2twoETUUz4j0dnHjaU5VU4_1E5Vh5uPWhrULoFBvnHgGVrqnStVOdyPaV1yII2VZeqo0nRIw9pn86Pu15m8bg9ZDOVghcDhhYo3OkR7lJRJ_9iZCaMDjEMJOsgmxcFLuhXsDSChx2gXD06Gso9SuC77qMewrUrs-jiDl24kDHLRXANeoKf8TmSgkUhNUNUw6lhWLlUNqWCB_o7ZiADmVGRn0y4xkzQQrIk2XpxxHOehcb4WZBO9pSQ7xh6v-a_XuaedjWm8guegczuB3Tjmi8ZBnZ%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1AwEFqqXcjoj26oT8N6wol9bYPT2t48T1NQwZruliDsSszhB3Ki4Na1o1bQMh4P_T_x5q4vx8RdYuR9gd8sV8kISy83JRlJU0-rb6XwDUqq43mbBqim84N0M0k8lS3dZsJh5PCTmLpEnbeGHsSgc093gW8HaOqq7MgaG2TC9TiSmcFR9An5Kgu6lQ50-ZC_S7k6yGlQTFL8vmPduk5xkgJnMSvgUuaN7NaCjfZeOnQaSvdFFl6yJp27HFA5Mdvlo3NCNHEWpc17QR4XxCXDZKoMO_a5ZY29UwGs8D-g_J73TmXh5A2G5v18P3tVv5Sz98%2525252Fhttps%252525253A%252525252F%252525252Fki.se%252525252Fen%252525252Fstaff%252525252Fdata-protection-policy%252526data%25253D04%2525257C01%2525257Cnilab.nasrullah%25252540stud.ki.se%2525257C24cbd9beba734a6d32ff08d9b3463b1f%2525257Cbff7eef1cf4b4f32be3da1dda043c05d%2525257C0%2525257C0%2525257C637737936493459886%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253DytHndbgsm01zT6kopWo0jOfiFxiExrAwUACsxeh34OA%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cnilab.nasrullah%2540stud.ki.se%257C7b67d760fc7a463d20f208d9bc3432e7%257Cbff7eef1cf4b4f32be3da1dda043c05d%257C0%257C0%257C637747754657965224%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D8A8xgtzL%252B6H0EbDwXPsm%252F2wxwW4v2l3ENE9TKHP%252FgR0%253D%26reserved%3D0>.
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<https://secure-web.cisco.com/1y18A7n363y7yxVLPw5RZ2YD1g7fRvx2t7C0vsofFeZ7VHAO2cTBenxOOgCo1BBzP_AVbRw1iOdXnOXyU4Y_wUbNk8OjFb9v-5SlLPHLqSWVwbBBhlUv32R2tUBXOaxqP_jmEVdMMhyj_WzuXd5tYk4X_XePJ59E26ZD5ybxi7eaOKQDBJ26yb-5xlmNiI17XY85Qf2T-WMn_GXVJH7WG1SP1_8Cqbh07PibQqwHFq9tbUH2MliHCiYoqi5dgPW8ZJua7WuEEsdws9yexoXHvNkOvPhAGS_BKmyAoNseqGGkKZLU73MafIhnfC82PNYli/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D04%257C01%257Cnilab.nasrullah%2540stud.ki.se%257C7b67d760fc7a463d20f208d9bc3432e7%257Cbff7eef1cf4b4f32be3da1dda043c05d%257C0%257C0%257C637747754657965224%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DNtxVu%252FfAbgRUKxWo%252BmvHWNIs%252BHvhK0K9y3nF9NFRNcU%253D%26reserved%3D0>
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/När du skickar e-post till Karolinska Institutet (KI) innebär detta
att KI kommer att behandla dina personuppgifter. /Här finns
information om hur KI behandlar personuppgifter
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/Sending email to Karolinska Institutet (KI) will result in KI
processing your personal data./ You can read more about KI’s
processing of personal data here
<https://secure-web.cisco.com/1XSdkvJKiVag4V9l-ah2EhvATa6_pLuG_oS92Rbd2DaJclGSQrgEDV5pcFGIWt_FqeFFGx-5z8y_s81zI9GtW5fQ7bq7yGdQI6vPe1zIw_OoDhHPSsE57euuJLc-AB04bymbOUaj6Z2C9I22f5SnHuwwmVsNFWrm4X-x3fyvvK5Y2KJ8d05n875O0WvGiszuYrGPpgLt3Efvl8YxQrA3RHHm-JoFQhOPCP5ytP4a7TnjII2Ibg_vyO8u_KYihErx_mi2U1R0vsn4E1SUhRJoRYkznmMvDSFjJGIVEGdYhA9llqiLAgSBqt_jTXzQNGKHk/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qHlChM2jTytSHjWPqLwrPCWHsOVbw3cf6Rd696VC3WQ-naSoa52ThU_EaRmuP7r4JBcVDVbnS_k9TAPF0xVOUgg7TgUATUTQIYK6rKmKVXCfr6dSecfp9toIb4NuMJldPjAXwe9l89UoO69vgCfPjhArnQw31AQN_FtiFBNZA2Xae3V1OzXGb1wj0sitf4stB_ZbsbBKLHjjqkjJbiUIrqyQ1O9u-uEYVJeQqpNtzkc55pPquzYQDplZhpjBVUxDm85NKRVVP9pgxGAol_Fp30jp9tQt-ChdO3HP3D0KbWp1acjFSOGrp-0r9pdSN0nm%252Fhttps%25253A%25252F%25252Fki.se%25252Fen%25252Fstaff%25252Fdata-protection-policy%26data%3D04%257C01%257Cnilab.nasrullah%2540stud.ki.se%257C7b67d760fc7a463d20f208d9bc3432e7%257Cbff7eef1cf4b4f32be3da1dda043c05d%257C0%257C0%257C637747754657965224%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DG5PcPQf8Yydu5Onu6Ifv0F4C4GE07Yh0Mu8OAvhbFf8%253D%26reserved%3D0>.
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
http://www.massgeneralbrigham.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.
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.
/När du skickar e-post till Karolinska Institutet (KI) innebär detta
att KI kommer att behandla dina personuppgifter. /Här finns
information om hur KI behandlar personuppgifter
<https://secure-web.cisco.com/1uYCbwFvSNCny8ogM5QvByWQ6yNVa8Gu49okGN28QybDYZIuvdLAK1jyyNTm_2Gau0e0eYfWahpL8Nwlr-KBIdoQlld9CrdNkMHV0_NKhaQPs7oUKysRO_sLqwLu7qDN1qeg3bt-zWw-il2pjVMOXbFp0ui1eq2LTN2Qcbo1k08CKYbEIhoTQpr2Z1CSZmSoxuZPKKn7YnOQHXXwKRgqhkh_nGp3S7FzQrVfxytR8qPZvibVGUEjMlT9_Hsj2AYhxmeaKb9mjd0_-r5xDoC_AuS_L_LGg9tRWt5wd_LQvACfLAxmq9tPdTPfCSsPdcv6D/https%3A%2F%2Fki.se%2Fmedarbetare%2Fintegritetsskyddspolicy>.
/Sending email to Karolinska Institutet (KI) will result in KI
processing your personal data./ You can read more about KI’s
processing of personal data here
<https://secure-web.cisco.com/15OVMmX7_h8cFCgKH4QAJFgj460fd4bU01WSe5GCTfSH5SN-bOeino2J9LeCPX4ONH1hFM6yd7etl0xp44HeZYwrMtQhmRexu-dzE1H5KHhVcqP7AGoBpBpVVTET70Rv0DLviozrStMxi08_IG4KJXaGLlXAiTRL4hXyoh8XRIEJdUvQKZRuwWykMtuRVixnAAnkruSxDtdKqn1L5NGHWF9v72XacmTnZ3xzOO5EYEiOdbMEShnqRf41qhQbCGSTmrNQn59bvF1u8JzyoUUh_YMa51XAKhgta8jy_WbYfTw2jGEpgNSv2AIJDc1I85RWn/https%3A%2F%2Fki.se%2Fen%2Fstaff%2Fdata-protection-policy>.
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contains patient information, please contact the Mass General Brigham
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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.
Please note that this e-mail is not secure (encrypted). If you do not wish to
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this message immediately. Continuing to send or respond to e-mail after
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