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 > 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. 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/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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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