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 PhDAssistant Professor of NeuroscienceInstitute 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/1RNwSit2rkfAZobK86FQ-0u2W7rCOisOJGNJUdXTjn4JJ_YYTEc5JfrFEULZiLkFuBHufgfdpKHdpMqnUv8zvjqfHCJR2rIHnmHtA-D8ugMIJRy9iJz0o-vcL3JGmXuBvnVtYjC3GelPiAUEhCPrpSeC065rIfDq5flQonzJ7AMYasSka968hktBTOEpmUxwNSGzp0b7LZXcoSOnynpezXd6sg9UGQnpQ1q92SLi4mG-ougxszyUvzXx14aTviYybE3wAQ1O1YTLZUHDGd_GyKeLeCmjnqJnozZbRW_l5BNHcTTm_dorYVy4VzLnEKjRTBdBua2iPb3b1NL1wsextrw/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 PhDAssistant Professor of NeuroscienceInstitute 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/1RNwSit2rkfAZobK86FQ-0u2W7rCOisOJGNJUdXTjn4JJ_YYTEc5JfrFEULZiLkFuBHufgfdpKHdpMqnUv8zvjqfHCJR2rIHnmHtA-D8ugMIJRy9iJz0o-vcL3JGmXuBvnVtYjC3GelPiAUEhCPrpSeC065rIfDq5flQonzJ7AMYasSka968hktBTOEpmUxwNSGzp0b7LZXcoSOnynpezXd6sg9UGQnpQ1q92SLi4mG-ougxszyUvzXx14aTviYybE3wAQ1O1YTLZUHDGd_GyKeLeCmjnqJnozZbRW_l5BNHcTTm_dorYVy4VzLnEKjRTBdBua2iPb3b1NL1wsextrw/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 > 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 > 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 > < > 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 PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
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