External Email - Use Caution Hi Anastasia :
I installed ANTS and tried this set ANTSPATH = /home/afrancis/Imaging/ANTs but it did not work. Is there a different set path? Thanks, Alan On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > If you want to use ANTs for registration, you have to have ANTs installed > and set ANTSPATH to its location. > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> > *Sent:* Friday, August 12, 2022 4:35 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Tracula - Preproc > > > External Email - Use Caution > > Hi Anastasia and King_Wei : > > Thank you for your suggestions. I have fixed the bet issue by reinstalling > FSL. But I have one more error: > > ERROR: must set ANTSPATH environment variable to use ANTs > > I tried setting > > set ANTSPATH = 0 but that did not work. > > I looked up the web to see if there were any default values I could use > for ANTs but did not come up with any. > > Thanks again for your help, > > Alan > > On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu <kingwai....@gmail.com> > wrote: > > External Email - Use Caution > > Hi Alan, > > If you really have FSL installed inside Freesurfer, it is not the way to > do it. > If you type > echo $FSLDIR > does it return anything? > If FSL is installed the way you said it is, echo $FSLDIR should give > something like > /usr/local/freesurfer/7.2.0-1/FSL > in your system > > Also, if you type > which bet > It should return something like > /usr/local/freesurfer/7.2.0-1/FSL/bin/bet > or type > ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet > Does it say "No such file or directory" or return > /usr/local/freesurfer/7.2.0-1/FSL/bin/bet > > If you don't get all these, your FSL is not installed correctly. > > Best, > > King-Wai > > On Fri, Aug 12, 2022 at 12:34 PM Alan Francis <alandarkene...@gmail.com> > wrote: > > External Email - Use Caution > > Hi Anastasia and King wei - > > I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL > is part of that installation. Do you recommend a second installation of FSL > separately? > > Thanks so much for your help and comments! > > Alan > > On Thu, Aug 11, 2022 at 2:50 PM <kingwai....@gmail.com> wrote: > > External Email - Use Caution > > Hi Alan, > > > > As Anastasia said, bet is part of FSL. > > If you don’t have it installed already, you need to install FSL. > > > > Best, > > > > King-Wai > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia > *Sent:* Thursday, August 11, 2022 3:42 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Tracula - Preproc > > > > Yes that's from FSL. It's needs to be in $FSLDIR. > ------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> > *Sent:* Thursday, August 11, 2022 3:30 PM > *To:* Freesurfer <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Tracula - Preproc > > > > * External Email - Use Caution * > > Hi Anastasia, King Wei: > > > > I did as you suggested with the config file and the preprocessing ran for > a bit but then an error occurred. I have attached the run script. It says > BET not found. Is this the Brain Extraction tool? > > > > Could you please shed some light on this? > > > > thanks so much, > > > > Alan > > > -- > > *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* > > > > > *Alan N. Francis PhD Assistant Professor of Neuroscience Institute of > Neuroscience* > > *University of Texas, School of Medicine* > > *Rio Grande Valley* > > *Texas.* > > > > _______________________________________________ > 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/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe2oToTdA6VNhB1sMV8WewODy8rtaT5aZgsHm4mn79Feu4jQV2PEL7D_56ZO680gA5g1VWd6Q9DMFVdkVg6T__bkr7lYT51johrjzh-7OUnNhpGGCz5bMwhHR_3vH5w3Fvx0CxzDc1OM0P3kdnRufUqDhnSIG6xtyhFRGaUF9HdVBPvSRMIxVbXXMBrw5ziw5cpjI-bhpnEJgIe9Z_aaMSh_jL-48zGleSExo_7q7vu1DoqsWuNwdf5DcjoSPEaTM0FLI3w1i_AzNKTcC8oL3-1bsyo2KnSAVYHOeuWLdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1jeB_jxkGKWxaafWD_KPYT2IRAgjmZbPF2GIUKKyvtF0_D3f3h4-FmZEPPt9Qlxio_CsG9mZaxY9l6gxc1MaZ1iWaodvNxwaCqKduHKs28N2e5-Ycc3MCG6UECKEzDxEG0UXLO8ukNiQwGgEvtS2-e8Svdio6FYyK1C7gtXoQcMpXR-IPcYaUbo0H8VOFKQIwfrheBtub-PMCrbzUzE-iUjRIbJiEH4f2uV4-blBzqVw-z1gFbivJ4DmwHoNYrb9CIBq2QHpqSQ_-TkUtUpKWGRi9GSaECcvVcox4xu6wwXOnLGGkGtRj1-BIJ7pSoe_wZR823aE7968dYs6eiAFnoA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > The information in this e-mail is intended only for the person to whom it > is addressed. 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Francis PhD Assistant Professor of Neuroscience Institute of > Neuroscience* > *University of Texas, School of Medicine* > > *Rio Grande Valley * > > *Texas. * > > > _______________________________________________ > 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/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe2oToTdA6VNhB1sMV8WewODy8rtaT5aZgsHm4mn79Feu4jQV2PEL7D_56ZO680gA5g1VWd6Q9DMFVdkVg6T__bkr7lYT51johrjzh-7OUnNhpGGCz5bMwhHR_3vH5w3Fvx0CxzDc1OM0P3kdnRufUqDhnSIG6xtyhFRGaUF9HdVBPvSRMIxVbXXMBrw5ziw5cpjI-bhpnEJgIe9Z_aaMSh_jL-48zGleSExo_7q7vu1DoqsWuNwdf5DcjoSPEaTM0FLI3w1i_AzNKTcC8oL3-1bsyo2KnSAVYHOeuWLdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1ya6JvGMaiTaLdV_RFI9p755zjyL9Xf7XygbVoLWjVcp1aMfCW54Ve6BXwyVTgw-sXgRlCbmWpM_HbJqT31X3b13LFy66hGznBK01PvWGqUimueqP9QVQYDFwMKYAt-U07t8W-9hFs5dcHM0tuz8fwSxvrgoEdY77mF3-sRfq_zNd6fLw9A_2iJlecVDkDmPNVs8t6YO5uEV2HK1MIO2GjjVBCgqOOAOroVb6ZNL5Y2hJus5WrH8CVwLBN5mijz1uxDoKZENg4ESJj8LMFh9_AYnIRkIenN3xWRP1hhC9yuBAAL732Uw4iEB7CAATwQSGjvqdGG1W_Opkjw8eqCL96A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > The information in this e-mail is intended only for the person to whom it > is addressed. 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Peters Dept. of Veterans Administration Medical Center (OOMH) > 130 W. Kingsbridge Road > Bronx, NY 10468 > _______________________________________________ > 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/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe2oToTdA6VNhB1sMV8WewODy8rtaT5aZgsHm4mn79Feu4jQV2PEL7D_56ZO680gA5g1VWd6Q9DMFVdkVg6T__bkr7lYT51johrjzh-7OUnNhpGGCz5bMwhHR_3vH5w3Fvx0CxzDc1OM0P3kdnRufUqDhnSIG6xtyhFRGaUF9HdVBPvSRMIxVbXXMBrw5ziw5cpjI-bhpnEJgIe9Z_aaMSh_jL-48zGleSExo_7q7vu1DoqsWuNwdf5DcjoSPEaTM0FLI3w1i_AzNKTcC8oL3-1bsyo2KnSAVYHOeuWLdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1RNwSit2rkfAZobK86FQ-0u2W7rCOisOJGNJUdXTjn4JJ_YYTEc5JfrFEULZiLkFuBHufgfdpKHdpMqnUv8zvjqfHCJR2rIHnmHtA-D8ugMIJRy9iJz0o-vcL3JGmXuBvnVtYjC3GelPiAUEhCPrpSeC065rIfDq5flQonzJ7AMYasSka968hktBTOEpmUxwNSGzp0b7LZXcoSOnynpezXd6sg9UGQnpQ1q92SLi4mG-ougxszyUvzXx14aTviYybE3wAQ1O1YTLZUHDGd_GyKeLeCmjnqJnozZbRW_l5BNHcTTm_dorYVy4VzLnEKjRTBdBua2iPb3b1NL1wsextrw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > 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 *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3HLlRVdVWN-74oApUxPN8znaISpUh1z-TdU9bzybFqWicJ2zbUOkTml-woSaYs6SJeEhq_Bu2Xl4zpX8J6EKn4SU5fiebbulJPmN4fZOyrNw94ykn4ZKYg6_e1yMhGH7NGHZD7iAVigvghReQ5wDN2ulbof78wEoRvZSdSmichjUWVkfaQaTS16UOGHjYzUygiFJpZJGmmpF4B0bHaJhaD8v3_v0HqDYUrOQqzcEgU7oFhxwwYDjTE009xxIztn5pWvraXm4zHxb-3zf2AC_l98unET5V35Tim1sF6s4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > <https://secure-web.cisco.com/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp31SW6-kYOnCnmeyVS-SE3eAA3Ull5x8RRKTtxftU2RRWsrFOo5o2I_JCZW7HlHoT25FyCUvZgmK9-DBS75-g0gUaJrzx5gwnGgN-SCmEjEopS1AKClT7mlI2BN_B5aolGTP3druy8C_K44PN_zmixRXyF5hT5AnGdLb77spGZ5dvm7aIp5Ehvzui3G1c7NIn6WQQ-j1bkQXc9qOAQ_4j6vgNoWGY6uAlCnKQtNLsq9nlGRs9mrrcKxDfsCcZ5Fe4rdtSk2VFAB64N49AoIt4RZbulQdF-tMh-ga2TFKtw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > <*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3HLlRVdVWN-74oApUxPN8znaISpUh1z-TdU9bzybFqWicJ2zbUOkTml-woSaYs6SJeEhq_Bu2Xl4zpX8J6EKn4SU5fiebbulJPmN4fZOyrNw94ykn4ZKYg6_e1yMhGH7NGHZD7iAVigvghReQ5wDN2ulbof78wEoRvZSdSmichjUWVkfaQaTS16UOGHjYzUygiFJpZJGmmpF4B0bHaJhaD8v3_v0HqDYUrOQqzcEgU7oFhxwwYDjTE009xxIztn5pWvraXm4zHxb-3zf2AC_l98unET5V35Tim1sF6s4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > <https://secure-web.cisco.com/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp31SW6-kYOnCnmeyVS-SE3eAA3Ull5x8RRKTtxftU2RRWsrFOo5o2I_JCZW7HlHoT25FyCUvZgmK9-DBS75-g0gUaJrzx5gwnGgN-SCmEjEopS1AKClT7mlI2BN_B5aolGTP3druy8C_K44PN_zmixRXyF5hT5AnGdLb77spGZ5dvm7aIp5Ehvzui3G1c7NIn6WQQ-j1bkQXc9qOAQ_4j6vgNoWGY6uAlCnKQtNLsq9nlGRs9mrrcKxDfsCcZ5Fe4rdtSk2VFAB64N49AoIt4RZbulQdF-tMh-ga2TFKtw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> > . > > > > -- > *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* > > > > * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of > Neuroscience* > *University of Texas, School of Medicine* > > *Rio Grande Valley * > > *Texas. * > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe2oToTdA6VNhB1sMV8WewODy8rtaT5aZgsHm4mn79Feu4jQV2PEL7D_56ZO680gA5g1VWd6Q9DMFVdkVg6T__bkr7lYT51johrjzh-7OUnNhpGGCz5bMwhHR_3vH5w3Fvx0CxzDc1OM0P3kdnRufUqDhnSIG6xtyhFRGaUF9HdVBPvSRMIxVbXXMBrw5ziw5cpjI-bhpnEJgIe9Z_aaMSh_jL-48zGleSExo_7q7vu1DoqsWuNwdf5DcjoSPEaTM0FLI3w1i_AzNKTcC8oL3-1bsyo2KnSAVYHOeuWLdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 > https://secure-web.cisco.com/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3HLlRVdVWN-74oApUxPN8znaISpUh1z-TdU9bzybFqWicJ2zbUOkTml-woSaYs6SJeEhq_Bu2Xl4zpX8J6EKn4SU5fiebbulJPmN4fZOyrNw94ykn4ZKYg6_e1yMhGH7NGHZD7iAVigvghReQ5wDN2ulbof78wEoRvZSdSmichjUWVkfaQaTS16UOGHjYzUygiFJpZJGmmpF4B0bHaJhaD8v3_v0HqDYUrOQqzcEgU7oFhxwwYDjTE009xxIztn5pWvraXm4zHxb-3zf2AC_l98unET5V35Tim1sF6s4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3HLlRVdVWN-74oApUxPN8znaISpUh1z-TdU9bzybFqWicJ2zbUOkTml-woSaYs6SJeEhq_Bu2Xl4zpX8J6EKn4SU5fiebbulJPmN4fZOyrNw94ykn4ZKYg6_e1yMhGH7NGHZD7iAVigvghReQ5wDN2ulbof78wEoRvZSdSmichjUWVkfaQaTS16UOGHjYzUygiFJpZJGmmpF4B0bHaJhaD8v3_v0HqDYUrOQqzcEgU7oFhxwwYDjTE009xxIztn5pWvraXm4zHxb-3zf2AC_l98unET5V35Tim1sF6s4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
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