External Email - Use Caution
Thank you so much King Wai,
On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionFor bash shell ANTSPATH=/home/afrancis/Imaging/ANTs
For tcsh setenv ANTSPATH /home/afrancis/Imaging/ANTs
On Fri, Aug 12, 2022 at 5:54 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHi 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 < AYENDIKI@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@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 CautionHi 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.chu@gmail.com wrote:
External Email - Use CautionHi 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 alandarkenergy@gmail.com wrote:
External Email - Use CautionHi 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.chu@gmail.com wrote:
External Email - Use CautionHi 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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@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
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*Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience*
*University of Texas, School of Medicine*
*Rio Grande Valley*
*Texas.*
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- 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/1tn-ndi6VMqb30krTJ0IxL8FNFb4DAL_SW6hagxu1X-0jPM... 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. 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/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/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/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JUBod6IgJGY-r-FiApP-1Qjq7IEcSiTDziBfRZ64RiYYgPhYh5mnBAPiA39QyviDts0LFEwFMad48dZN_wbbt-XzotWZl-fXA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
-- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. 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/1tn-ndi6VMqb30krTJ0IxL8FNFb4DAL_SW6hagxu1X-0jPM... 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/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... 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/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... 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> .
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- Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley *
*Texas. *
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*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley*
*Texas.*
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-- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. 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/1tn-ndi6VMqb30krTJ0IxL8FNFb4DAL_SW6hagxu1X-0jPM... 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/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... < https://secure-web.cisco.com/1ew4HkjVDBWlLOJWjKzTPqDARpmpvjBZxKJCBR1vgHtyisK... .