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Dear Freesurfer team,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
Also, I have read there is an example of segmentation that comes with FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
Your help on this is very much appreciated
Kind regards, Rosie
External Email - Use Caution
Hi Rosie,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
There are a few tutorials that may be helpful (a full list of tutorials is here https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4Z...)
- Introduction to Freesurfer Output ( https://secure-web.cisco.com/18uPMHpt-EW_7l-sGIaivhnHa95jFiH6KEsNWb04DvYfYf5...) - Troubleshooting your output ( https://secure-web.cisco.com/1zI67HQZxy9cLn2I7uNmt2Vr-hMBP6KFcnjs-2A6egLkEI1...) - Quality Check a FreeSurfer Recon Demo ( https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGyw...)
Also, I have read there is an example of segmentation that comes with
FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
There should be an example that comes with the FreeSurfer installation. I can't remember exactly what comes with v6, but you should find more info with `cat $FREESURFER_HOME/subjects/README`
Good luck!
-Paul
External Email - Use Caution
Thank you!
Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
There are a few tutorials that may be helpful (a full list of tutorials is here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1V1LcsFSf2XB35bDn5z1UxdX3hNx-6KYEWloSkJdLjgvZB8... https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4ZPQZOCVExtqPxRRAOWBluRDRjQqno9QrifD6CT8o6C91nxLIK51ygwiD_a39suQIFvjfTIAwewDsrBzOPd0KafjQda5FJFwreS1HTt1HosPKu8vwfBtxK_-pjMFsWnozXAMp9NfzqiKFBVYdRwC2tKzjM4egHuUwi4z9lf6LD2g73pypGrmcJy2WLqaqKyrv8HZQznR_0PD-S2Yvn_wIR0dwiBFmkDXRxUl-Q8v_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials )
- Introduction to Freesurfer Output (*MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1vOyI1dhfeKyBGSUWawwFgRKcrqKlVxUVE64EToPPpdCPOJ... https://secure-web.cisco.com/18uPMHpt-EW_7l-sGIaivhnHa95jFiH6KEsNWb04DvYfYf5ZGlM1P6TunxF4ua8lyLPmgu4nvzTMwzZcdxgpYY5VayEiZvGZqVbJZ5D2JYEF5oTJxv7waaXt3YGX6jWknB4IjYDcr0omjY4c3L9yXXHLouBDOyWD-y-S2XtFdj5rSiS32CBQr9fuottLqbP1ApRZsrxO2C2BQY3-BldhPPwZuf5BG1Wk8kfubSeTdsQY5oHR0a_5P2pa15O22b_v8f96s2PK40XcUbmIyZJr2Pg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview )
- Troubleshooting your output (*MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/18iwLDYpb6cxV1Dt_02A8aGYx_BXWW49ifXqIly-9fCK6PG... https://secure-web.cisco.com/1zI67HQZxy9cLn2I7uNmt2Vr-hMBP6KFcnjs-2A6egLkEI1MdK1Gq5cjgRVpOKFeY0BZHSQpCxQ_hvmo-1q_fm4W5LBFlzeRGLRkMeqnlLkCjVUHD91Mg4XY5bp69Vv4H6Ki2R5vSBBt-vqF1FTgrVYSdUrw2DT9R9zxt4y9rWxSh5-0__pOG9knY3Wo_iwk1tqsMMeTL6-stQkgJwC6RUi7qglYapWN7yyR5yIfYachGm9H6TULtIlGONzwBDlLjpFHrzKvuV3VeugenXt3RuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData )
- Quality Check a FreeSurfer Recon Demo (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1g-1kV9dX2QoF9kKP-5m6ew_znGKAWoFJID9fae6RUBMfY9... https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGywKINhle2vo9kPS3sRJshRi7RBTgT3m5i4YzA51pzGB9J7ozBiNK_3EJYqP80jsPsR2MgunkxzNuzhwrWyjyAkDaKuii2Ak2stl5dJifUtwrZ80fr8twb486IsKisN8ktU2NQ-NBSzVzwIcltDwaBTYGPzQrKb2zwAXiXm-V3z4TdghHvMclkYac6iKI1Y70xc6GPHROPaVuBFPqBIGI4chLrGmPOYRQ_r6QDW9VtA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ )
Also, I have read there is an example of segmentation that comes with
FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
There should be an example that comes with the FreeSurfer installation. I can't remember exactly what comes with v6, but you should find more info with `cat $FREESURFER_HOME/subjects/README`
Good luck!
-Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1nreO8i4IHPbmoU20Xg705eE14iD2vBzX4jqCbCfAIAUi3t...
External Email - Use Caution
Hi Paul,
Not sure what command I should run when I edit the brainmask because the pial got too much.
Kind regards, Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
There are a few tutorials that may be helpful (a full list of tutorials is here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1KKtU14lfEF2p4D2eFjLuFeNgwDDSY3YYh8tQDtHUAaGyqD... https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4ZPQZOCVExtqPxRRAOWBluRDRjQqno9QrifD6CT8o6C91nxLIK51ygwiD_a39suQIFvjfTIAwewDsrBzOPd0KafjQda5FJFwreS1HTt1HosPKu8vwfBtxK_-pjMFsWnozXAMp9NfzqiKFBVYdRwC2tKzjM4egHuUwi4z9lf6LD2g73pypGrmcJy2WLqaqKyrv8HZQznR_0PD-S2Yvn_wIR0dwiBFmkDXRxUl-Q8v_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials )
- Introduction to Freesurfer Output (*MailScanner has detected a possible
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- Troubleshooting your output (*MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1lV0fxZL0BMC9xPLoF4ZmBC_y6-f-8pfzbd1a4Ma3P0e9md... https://secure-web.cisco.com/1zI67HQZxy9cLn2I7uNmt2Vr-hMBP6KFcnjs-2A6egLkEI1MdK1Gq5cjgRVpOKFeY0BZHSQpCxQ_hvmo-1q_fm4W5LBFlzeRGLRkMeqnlLkCjVUHD91Mg4XY5bp69Vv4H6Ki2R5vSBBt-vqF1FTgrVYSdUrw2DT9R9zxt4y9rWxSh5-0__pOG9knY3Wo_iwk1tqsMMeTL6-stQkgJwC6RUi7qglYapWN7yyR5yIfYachGm9H6TULtIlGONzwBDlLjpFHrzKvuV3VeugenXt3RuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData )
- Quality Check a FreeSurfer Recon Demo (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1LJ8OCErnRX1PHiErdWFjzl0M0aLTJpPR6JECKTqfxToV_I... https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGywKINhle2vo9kPS3sRJshRi7RBTgT3m5i4YzA51pzGB9J7ozBiNK_3EJYqP80jsPsR2MgunkxzNuzhwrWyjyAkDaKuii2Ak2stl5dJifUtwrZ80fr8twb486IsKisN8ktU2NQ-NBSzVzwIcltDwaBTYGPzQrKb2zwAXiXm-V3z4TdghHvMclkYac6iKI1Y70xc6GPHROPaVuBFPqBIGI4chLrGmPOYRQ_r6QDW9VtA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ )
Also, I have read there is an example of segmentation that comes with
FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
There should be an example that comes with the FreeSurfer installation. I can't remember exactly what comes with v6, but you should find more info with `cat $FREESURFER_HOME/subjects/README`
Good luck!
-Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DHbxGoPwPUUJCixsnh0mQrCQIauHUV98bwCgaNLKb83X09...
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Hi Rosie,
I'm going to have to defer to others about questions on manual editing.. I've never done it!
Sorry,
-Paul
On Thu, Jul 8, 2021 at 1:27 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Not sure what command I should run when I edit the brainmask because the pial got too much.
Kind regards, Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
There are a few tutorials that may be helpful (a full list of tutorials is here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1czW6pKBcE24-CNRkxb6ooGpRPNjnMWsjYmV1Vm5VwXhF19... https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4ZPQZOCVExtqPxRRAOWBluRDRjQqno9QrifD6CT8o6C91nxLIK51ygwiD_a39suQIFvjfTIAwewDsrBzOPd0KafjQda5FJFwreS1HTt1HosPKu8vwfBtxK_-pjMFsWnozXAMp9NfzqiKFBVYdRwC2tKzjM4egHuUwi4z9lf6LD2g73pypGrmcJy2WLqaqKyrv8HZQznR_0PD-S2Yvn_wIR0dwiBFmkDXRxUl-Q8v_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials )
- Introduction to Freesurfer Output (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Y4PmXm9jm0p3BdjnWrwYX4tVbC0r8t0gnjlMQI8M8MboDr... https://secure-web.cisco.com/18uPMHpt-EW_7l-sGIaivhnHa95jFiH6KEsNWb04DvYfYf5ZGlM1P6TunxF4ua8lyLPmgu4nvzTMwzZcdxgpYY5VayEiZvGZqVbJZ5D2JYEF5oTJxv7waaXt3YGX6jWknB4IjYDcr0omjY4c3L9yXXHLouBDOyWD-y-S2XtFdj5rSiS32CBQr9fuottLqbP1ApRZsrxO2C2BQY3-BldhPPwZuf5BG1Wk8kfubSeTdsQY5oHR0a_5P2pa15O22b_v8f96s2PK40XcUbmIyZJr2Pg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview )
- Troubleshooting your output (*MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/17yG4rWY2JH-aueRtfCzJBhm5PI3rbAKiXFr2EQ9XFJf8sN... https://secure-web.cisco.com/1zI67HQZxy9cLn2I7uNmt2Vr-hMBP6KFcnjs-2A6egLkEI1MdK1Gq5cjgRVpOKFeY0BZHSQpCxQ_hvmo-1q_fm4W5LBFlzeRGLRkMeqnlLkCjVUHD91Mg4XY5bp69Vv4H6Ki2R5vSBBt-vqF1FTgrVYSdUrw2DT9R9zxt4y9rWxSh5-0__pOG9knY3Wo_iwk1tqsMMeTL6-stQkgJwC6RUi7qglYapWN7yyR5yIfYachGm9H6TULtIlGONzwBDlLjpFHrzKvuV3VeugenXt3RuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData )
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possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1nlexAM5p5xH0PFNwe-wszdujC8ps20WrOdXBNj2DUuBJiE... https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGywKINhle2vo9kPS3sRJshRi7RBTgT3m5i4YzA51pzGB9J7ozBiNK_3EJYqP80jsPsR2MgunkxzNuzhwrWyjyAkDaKuii2Ak2stl5dJifUtwrZ80fr8twb486IsKisN8ktU2NQ-NBSzVzwIcltDwaBTYGPzQrKb2zwAXiXm-V3z4TdghHvMclkYac6iKI1Y70xc6GPHROPaVuBFPqBIGI4chLrGmPOYRQ_r6QDW9VtA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ )
Also, I have read there is an example of segmentation that comes with
FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
There should be an example that comes with the FreeSurfer installation. I can't remember exactly what comes with v6, but you should find more info with `cat $FREESURFER_HOME/subjects/README`
Good luck!
-Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/112Glt1gX_olau1BV9wt47Kjp-lYXwPtZPmaB7dVahHaKCP... https://secure-web.cisco.com/1DHbxGoPwPUUJCixsnh0mQrCQIauHUV98bwCgaNLKb83X09xBfK7o3X7Uj5F1Y6vzxIjPlgV3ZT2vp7aXbVPuSqFUlzb0B7FLzyGgqeZqPmkAJjw3lKAfF7RIsCffMVJ9jCBMQA-Vgekre5xLOi3QnMERQYAK1OVgBr2yQOkgGEPmchh-WHSaNpec76HTrPZ0oPHAfDDUZzQuwMJ7eLtNnMV9QlgJrwqumWlesuSvss-zlM0815iNPvDqSGyL7Og3ArkzucOeLoxq2I9Zkh3aAQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/112Glt1gX_olau1BV9wt47Kjp-lYXwPtZPmaB7dVahHaKCP...
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The troubleshooting tutorial suggest running
freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red
so you could try:
cd $SUBJECTS_DIR
then the command above, replacing "pial_edits_before" with the subject name.
That's just a guess though!
-Paul
On Thu, Jul 8, 2021 at 1:42 PM Paul Wighton paul@corticometrics.com wrote:
Hi Rosie,
I'm going to have to defer to others about questions on manual editing.. I've never done it!
Sorry,
-Paul
On Thu, Jul 8, 2021 at 1:27 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Not sure what command I should run when I edit the brainmask because the pial got too much.
Kind regards, Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
It is my first time editing wm segmentation (white matter segmentation errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
There are a few tutorials that may be helpful (a full list of tutorials is here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1FqGVAMeNL5hJdBdkvAEoeHuxpMZudV_B2U6yCU8J739tKU... https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4ZPQZOCVExtqPxRRAOWBluRDRjQqno9QrifD6CT8o6C91nxLIK51ygwiD_a39suQIFvjfTIAwewDsrBzOPd0KafjQda5FJFwreS1HTt1HosPKu8vwfBtxK_-pjMFsWnozXAMp9NfzqiKFBVYdRwC2tKzjM4egHuUwi4z9lf6LD2g73pypGrmcJy2WLqaqKyrv8HZQznR_0PD-S2Yvn_wIR0dwiBFmkDXRxUl-Q8v_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials )
- Introduction to Freesurfer Output (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Dm8vbyuLMvXsp37wgx1-nCVZ7Hb-WKI2f_Gr-mmPtBriel... https://secure-web.cisco.com/18uPMHpt-EW_7l-sGIaivhnHa95jFiH6KEsNWb04DvYfYf5ZGlM1P6TunxF4ua8lyLPmgu4nvzTMwzZcdxgpYY5VayEiZvGZqVbJZ5D2JYEF5oTJxv7waaXt3YGX6jWknB4IjYDcr0omjY4c3L9yXXHLouBDOyWD-y-S2XtFdj5rSiS32CBQr9fuottLqbP1ApRZsrxO2C2BQY3-BldhPPwZuf5BG1Wk8kfubSeTdsQY5oHR0a_5P2pa15O22b_v8f96s2PK40XcUbmIyZJr2Pg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview )
- Troubleshooting your output (*MailScanner has detected a possible
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- Quality Check a FreeSurfer Recon Demo (*MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/18r3epGj9vM1hoKTfnVG1o8XH7cTV_OZu2QIYNNCRAJWaok... https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGywKINhle2vo9kPS3sRJshRi7RBTgT3m5i4YzA51pzGB9J7ozBiNK_3EJYqP80jsPsR2MgunkxzNuzhwrWyjyAkDaKuii2Ak2stl5dJifUtwrZ80fr8twb486IsKisN8ktU2NQ-NBSzVzwIcltDwaBTYGPzQrKb2zwAXiXm-V3z4TdghHvMclkYac6iKI1Y70xc6GPHROPaVuBFPqBIGI4chLrGmPOYRQ_r6QDW9VtA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ )
Also, I have read there is an example of segmentation that comes with
FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example.
There should be an example that comes with the FreeSurfer installation. I can't remember exactly what comes with v6, but you should find more info with `cat $FREESURFER_HOME/subjects/README`
Good luck!
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Paul Wighton -
Rosalia Dacosta Aguayo