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Hello,
I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask.
Thanks for your help, Irene Balboni PhD student She/Her
Institute de plurilinguismehttps://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duHGk4rhiIzM9LB0z7YfOSEvpcpUW2Vvrg-ISqJbvImgtoneLSk8oyjNXZPhv9YQEwck2mFdw3ySjyETxvAv2nlmsAPBJkQajh7MI4E0Gv1dFV0ot3za9MbRcUcRFMVwLZEkh8uP84QVf3-KcqehV6YFJt0EhNNvpBJqbgsMw1HNHFrtLdAQWC8Ub9CaX_S4oR9el-UFqav5WaW5zc3Q75xC10lNWkbNE1HeF6fpKNV-jirieoG2h9Hynul-tpf9-dRloyKXl31VY1gGmCt4Bi/https%3A%2F%2Finstitut-plurilinguisme.ch%2Ffr | Université de Fribourg & Brain and Language Labhttp://secure-web.cisco.com/1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xjv7w_XKOZTQwQroW2KcI5WX5cXFMQQJWl9OcTsgzpK7bGjmql6hhHKNFs8qkbuKMt2gjuAJZEU5FkAgZSQMx1fr8YjMRC8HHFdM0XG_37kdDWmcGIz99U_EaKBkam1Nvh4xaosCMELtOn_ciQcmmKP52TS9tR4y3g9eeb-I7l1_C2v_dGzoy_uJJDakwvACjHuIQp05m1s4zhCgGFIroxRCIOp51LMXOpoXO5QEj9hbTN1qVPrel7L9x67zif7l1PFiyel0Ut1uiyHN-2CE/http%3A%2F%2Fbrainandlanguagelab.org%2F | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141
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This is from Freesurfer wiki - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQhttps://secure-web.cisco.com/1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e1KlQ28-1bqlh2D9mdfR4oz5K2DcAapaDi_kIRYa9oOGpUGPN7HBgvT7nsrqBOhDSS1cOpeZ1vlmzNwZczc-cKlN2aymuKdjRBszVXj6pSIzy284SpTKycNB0Fu9kYvlF9WMrQLPBazYr7itkxhkOU3JWMD4-UoiVa9TbyhR71UonTZDQK57ox2IABmOi_Byg-ahMf7rWMa3NdavabkZhRt_6s9jZZE9ooyzXY-aFh0m-UBLCJJ5H-q_XO5-sie0nuzq8b8Z2HV6a3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUserContributions%2FFAQ Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently. First you must run only -autorecon1 like this: recon-all -autorecon1 -noskullstrip -s <subjid> Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all: recon-all -autrecon2 -autorecon3 -s <subjid> Hope it helps. Best, Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of BALBONI Irene Sent: Tuesday, December 19, 2023 3:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon all with optiBET brain mask
External Email - Use Caution Hello,
I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask.
Thanks for your help, Irene Balboni PhD student She/Her
Institute de plurilinguismehttps://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duHGk4rhiIzM9LB0z7YfOSEvpcpUW2Vvrg-ISqJbvImgtoneLSk8oyjNXZPhv9YQEwck2mFdw3ySjyETxvAv2nlmsAPBJkQajh7MI4E0Gv1dFV0ot3za9MbRcUcRFMVwLZEkh8uP84QVf3-KcqehV6YFJt0EhNNvpBJqbgsMw1HNHFrtLdAQWC8Ub9CaX_S4oR9el-UFqav5WaW5zc3Q75xC10lNWkbNE1HeF6fpKNV-jirieoG2h9Hynul-tpf9-dRloyKXl31VY1gGmCt4Bi/https%3A%2F%2Finstitut-plurilinguisme.ch%2Ffr | Université de Fribourg & Brain and Language Labhttp://secure-web.cisco.com/1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xjv7w_XKOZTQwQroW2KcI5WX5cXFMQQJWl9OcTsgzpK7bGjmql6hhHKNFs8qkbuKMt2gjuAJZEU5FkAgZSQMx1fr8YjMRC8HHFdM0XG_37kdDWmcGIz99U_EaKBkam1Nvh4xaosCMELtOn_ciQcmmKP52TS9tR4y3g9eeb-I7l1_C2v_dGzoy_uJJDakwvACjHuIQp05m1s4zhCgGFIroxRCIOp51LMXOpoXO5QEj9hbTN1qVPrel7L9x67zif7l1PFiyel0Ut1uiyHN-2CE/http%3A%2F%2Fbrainandlanguagelab.org%2F | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141
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External Email - Use Caution
Dear Yujing, Thank you for your reply. Would there be a way to just use the mask created with optiBET for the recon-all process to mask the brain? At the moment we are segmenting 2 images at once (mprage and mp2rage) to improve the quality of the segmentation and we have the skull-stripped images only for one of them so the solution below might not be ideal.
Thanks again.
Best, Irene
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: venerdì 29 dicembre 2023 15:44 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all with optiBET brain mask
This is from Freesurfer wiki - MailScanner has detected a possible fraud attempt from "secure-web. cisco. com" claiming to be https: //surfer. nmr. mgh. harvard. edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped data. Can
This is from Freesurfer wiki - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hcYnA9bt1-Vcu45hvleS0donbIaySbZpKWJuHfsnXO8nzz...https://secure-web.cisco.com/1tu630hE3EjDp_haYNYF6LD6KROQHLIzgLG2YW2r4AERBi9Le_GX2QSVu-x45Qv0YHxGYpACPN9wsvTACzaTa0f3R2lF49sUIzm_bvNOqHxZejuHRbadTG_BnhDr_s7O61j-x4qKWqUqQPPLVgawRh1SVUGMeTBhbuBzUE6FkTI0uAu8JE7KDMdnOM9-n4LOcoK9dsS7t2Tmx0uJgi-NsFmkAbNppylb2oc26pktuWeH-k5zm8epCnnHQ6yovd7CYq-3qL8ryed4kpvQBETYhvwpY4WpkVhue1Brn2CguSsPwmk5gu-5VyhNTxcOxnwvI6Rva7m3dxC1aWYWVqo_3QQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e1KlQ28-1bqlh2D9mdfR4oz5K2DcAapaDi_kIRYa9oOGpUGPN7HBgvT7nsrqBOhDSS1cOpeZ1vlmzNwZczc-cKlN2aymuKdjRBszVXj6pSIzy284SpTKycNB0Fu9kYvlF9WMrQLPBazYr7itkxhkOU3JWMD4-UoiVa9TbyhR71UonTZDQK57ox2IABmOi_Byg-ahMf7rWMa3NdavabkZhRt_6s9jZZE9ooyzXY-aFh0m-UBLCJJ5H-q_XO5-sie0nuzq8b8Z2HV6a3Q%2Fhttps*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FUserContributions*2FFAQ__;JSUlJSUl!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodUCCthFB$ Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently. First you must run only -autorecon1 like this: recon-all -autorecon1 -noskullstrip -s <subjid> Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all: recon-all -autrecon2 -autorecon3 -s <subjid> Hope it helps. Best, Yujing
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 BALBONI Irene Sent: Tuesday, December 19, 2023 3:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon all with optiBET brain mask
External Email - Use Caution Hello,
I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask.
Thanks for your help, Irene Balboni PhD student She/Her
Institute de plurilinguismehttps://secure-web.cisco.com/1I_JnpDzyOEyx8Jc7K_q3g5IPB7KbXj-76l10Sg_ahaccSisgZ9e4iRurQRSsDvbTxAJ4xB1aUPEPKI_zZFEhxC76_IqIj2_J54iaGtEBmn3s20exzRYq6Kyi-0-HV6J5aypu0Zjn_ybfK34BZnCGYrStB1CN9gA67c7-nxePl9CW0m8oRFAimAy9xfsSd4-2AHkjffvE-6TaCMjfUWgkFzynqchCnkaQ2QOoasJTkMdcVGoVKYJpbubqx6lFduXwWsec74DTxrnBBQOg-VMbnEBcA0olXJ60rb1L_PRitAapjnHmwrfP8ja7FpPtja5VNnohaRQdWU76qufEXOhQNw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duHGk4rhiIzM9LB0z7YfOSEvpcpUW2Vvrg-ISqJbvImgtoneLSk8oyjNXZPhv9YQEwck2mFdw3ySjyETxvAv2nlmsAPBJkQajh7MI4E0Gv1dFV0ot3za9MbRcUcRFMVwLZEkh8uP84QVf3-KcqehV6YFJt0EhNNvpBJqbgsMw1HNHFrtLdAQWC8Ub9CaX_S4oR9el-UFqav5WaW5zc3Q75xC10lNWkbNE1HeF6fpKNV-jirieoG2h9Hynul-tpf9-dRloyKXl31VY1gGmCt4Bi%2Fhttps*3A*2F*2Finstitut-plurilinguisme.ch*2Ffr__;JSUlJQ!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodRX4idJ3$ | Université de Fribourg & Brain and Language Labhttps://secure-web.cisco.com/1Ym-b_vy__wQGC_nV8xTI1qGa-OJCSfYy-q3NnfW5Idd9hzC8yw1eGaEN96maJRXrVphWNFoSrJh2F-S2eL-eRFY2KP9769KsQ9Mt7NpZn209vgYJ5oi0FyLNnLVwveiuomUDeS7FWi817CAUWJYm_VgbudfbFA_onFAym9mVRGlt2OZSRT_TogSABJa5Vr1Vtl5QF2x_utJmGSM3eao3w35MkPEjmGeRAznQ0eEnyBIncsBh8Rr1oMcAfl0a52iHfbrErfLyOMXu6l82H26DtDOtazEjWK_HtxG_SBdw4uZijWnNGi_5E5zj_2RQmVIGIdzEi7Fe-FGcv-v1bi4O3Q/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xjv7w_XKOZTQwQroW2KcI5WX5cXFMQQJWl9OcTsgzpK7bGjmql6hhHKNFs8qkbuKMt2gjuAJZEU5FkAgZSQMx1fr8YjMRC8HHFdM0XG_37kdDWmcGIz99U_EaKBkam1Nvh4xaosCMELtOn_ciQcmmKP52TS9tR4y3g9eeb-I7l1_C2v_dGzoy_uJJDakwvACjHuIQp05m1s4zhCgGFIroxRCIOp51LMXOpoXO5QEj9hbTN1qVPrel7L9x67zif7l1PFiyel0Ut1uiyHN-2CE%2Fhttp*3A*2F*2Fbrainandlanguagelab.org*2F__;JSUlJQ!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodfBFW57p$ | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141
Twitterhttps://secure-web.cisco.com/19xxbna1mSz1qD_3SWsYFchdFiTA0QSHYstRlHzj2HgRdwlKoVOid1EF8chRUhyUA6NQawyRiufkRDF_0lnIsZ3dmOxWrFRu-gNhEOU19fRWPkml6XgdJBu614nEwnXN_VqEsTsyALH94pKj-eR9yBW4ZIVf7Hhrb4J9ZJVwSNMQWPrDERgAJzzi1LXdtEOg7OuoNqEqT-0fmMaNB5aUnQTuQnYc2KT2AjM-L1LdjfXjT1LSMIco7CpMgNxl4fqLJRmNISSIFi9_OoW032Xw_a5zqlhEIjm2fIJH0AuCaXE-QfWZHX0qWivBJ6RgTJDS4CWLw1u23Q6kBGfb4oXF1VA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F17WKW8eFYGf6kC7ikhhz87_g3_OExqqtlPMTRdUfjaGR0uluTiqaXYJbfgje5xkN0AGUHCzqJvTMeOwIAoh_bIDXnFSl787LpKfXLOhqGoxeoeVXVoYnxhRn0IdG-m1365IFFI1HCl6lU6gR1MJUm03GRxwDOn1c58BqO2RNNAsj-n5_nXvmgc-Qk5tXs9dyCT93UY0FeiN8ejIl0NsIhreKkKGvoagzjD_d6k_pe_bAXTknyxKPD2WEeYA5rdplIaDcGLJcpkHfiNG4Vi8g3TQwYtJdUPDfJlWv0-kb0vQMk2l2c5zWftzhtmBEeaXLL%2Fhttps*3A*2F*2Ftwitter.com*2Firene_balboni__;JSUlJQ!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodSVn2hRs$ | ResearchGatehttps://secure-web.cisco.com/1TOI4JRKOZPWYKKsV1zBJHReWdjrgx6DrHzmpAWAXPUep21S2UPA48WBPlE-I95j1EGK8rkNTS86JX_RZQQrOi3GT_sDGTkFdERpLxhwil0iqhOMUfZiOAC1hGVhvQ5Q-ZKZnqEfvXCqAb_m9p6YrmM8tyvn5iybNgyVYPJFEugrDFI5KcbGJdr1XIijw7z_uXaTla7gcjWU8FNGPtVsgG_k0epm4Kp6D9oCy-6UfE84xDbjXMhIXM9d5fYZ_ZS79EaNoO6i06QoKXUJT-TG97m4uFXKninktmd1YvOktiih0X05ZqXrj9MKvDjL96GRuWvDWaGfRuemt3g8LVJmjfA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F17QR3OuPCdu6j4aAtW1iy0qnt2WV8MA0yHG3gonUNgbpnoytFe_OT2t_PeZLUNBCumnPO91xKpUoHW2nXZ2GLpe3ACdRR0awLiFb_A2if5t1mgNBmYhmPmQ2jczQZTFIOs0XkQvfnIdJRFWvyyoH2AZ8ptXXCk-e9rv6j77b5YAFYk93jEuAXmpaqX5apol2w74ZvDxE5_sUBQ3FKXYE80cgKupAg62LC7S1PhHk91JDw_whVgbjFHy2H0_UGQKN6HoUGevumgUsd3HFsTPZ1ptbFf3_Ei3S80w4HVA3kRjjlKgssCFRQmy2zMX6wqzfe%2Fhttps*3A*2F*2Fwww.researchgate.net*2Fprofile*2FIrene-Balboni-3__;JSUlJSU!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodTrmz5ce$ | Linkedinhttps://secure-web.cisco.com/1ZC22YZBU7wRFlDAw_VioKFr4C17Lp0ArVR-kEAqja1r7m1EYvIuP9pmfLgAu6f8FsjTH95gPCw-CGatIisQxGrLTy6kxhMVEV1MpD7QtHuNtwoYK7h7bP8McfaHhtuOgKszfjDHcWXyTvLouc_6hA_Q2E2avNy0X6-vlKj6_ml1uxipBsQ4H1xuVrYVcB6mqzPG1ShZ2Prw5iVo_cP5RqD-wh4TID_UVuLanA7lGYy14VJVlYK-I1eOUYDA799Er674ChuGvOomCLt3B8U236d5Vb56TfEZOxLiUfhm0HwQMdvMtxpG0A1xv6fGrpPnmJVub_lMUZvxh6nfk4oJfYQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F10d7bSA4mUh4az6x-hBwYc5c1373f-jWI1YMV5SjB-YHxEpSfF44wijFghbzodwriULKShKPeEp7GuGZIehjLR-AsJCmC8_am5bUFDDbn4Emi60hYMnjRxmCknyJw7B8YjyVRAb7v6fgqYkHFbauczQ89026CBfsNDyuE3ZSZU6eniJbceQI2zjkPWje7Su8bLiWLYb-BSWQi0sInsSwyR06qqHeJIE96hEiKBWs4LhqxLsiGCOClB27Ot0RxAk4dnV8KvFvgLvFoGRnu7PRu1gJr95fCha_TVRSxQ1lsbYguORGstmdfXHbGqYTxIkYg%2Fhttps*3A*2F*2Fwww.linkedin.com*2Fin*2Firene-balboni-72b533196*2F__;JSUlJSUl!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodZD-QR68$
freesurfer@nmr.mgh.harvard.edu
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BALBONI Irene -
Huang, Yujing