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-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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Alan Francis <alandarkenergy@gmail.com mailto:alandarkenergy@gmail.com > Sent: Thursday, August 11, 2022 3:30 PM To: Freesurfer <freesurfer@nmr.mgh.harvard.edu mailto: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

The error message that you got says that the bet command isn't in your Unix path. You need to fix that, so that you don't get that error. If bet and all the other FSL executables are already installed somewhere on your computer, you need to add that directory to your Unix path. I'm not sure what "It shows that FSL is part of that installation" means (what does "it" refer to?), but if "which bet" doesn't show you a directory where bet can be found, you won't be able to get any further. ________________________________ 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 12:33 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula - Preproc

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.chu@gmail.commailto:kingwai.chu@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-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 Yendiki, Anastasia Sent: Thursday, August 11, 2022 3:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> Sent: Thursday, August 11, 2022 3:30 PM To: Freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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.

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.chu@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 alandarkenergy@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.chu@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-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

--

*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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_Y... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... 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.*

---

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_Y... 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/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... 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/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... 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 https://secure-web.cisco.com/1RNwSit2rkfAZobK86FQ-0u2W7rCOisOJGNJUdXTjn4JJ_Y... 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/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... < https://secure-web.cisco.com/1NoQSBD7koFWxXVGA1fxFK5Y8knUpyMW5dA0irD183jfqp3... .

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 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 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.chu@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 alandarkenergy@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.chu@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-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

--

*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe... 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/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3... 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/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3... 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/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe... 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_0GaVoGCxxOjK3... 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_0GaVoGCxxOjK3... 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_N1l7oRm0rXzQZrFiO9Qe... 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_0GaVoGCxxOjK3... < https://secure-web.cisco.com/10JAZPF9TK94uvIg4HC-gnf5j-d_MzwRu_0GaVoGCxxOjK3... .

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 Caution

For 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 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 < 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 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.chu@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 alandarkenergy@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.chu@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-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

--

*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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. *

---

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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 *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> .

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

• 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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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/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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 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... .

External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis alandarkenergy@gmail.com wrote:

    External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found. Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the *antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis alandarkenergy@gmail.com wrote:

...

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 Caution

For 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 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 < 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.

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*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 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.chu@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 < alandarkenergy@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.chu@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-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

--

*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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 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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... 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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... 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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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 <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... 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.*

---

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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... https://secure-web.cisco.com/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... https://secure-web.cisco.com/1kUg_dV0QxDtOWXilrxzAoM8AieGG16geE84CUkUAZzdBNmHrOjZZDtFeqUbxS5mjlbcxCHNpTRj01p9ynfe48PGFr7KvT2dMtVSPYyM4FQvClwqQv_NBRB5-d07oeTv2SibOzGSHo_8N4XXmVk022xGDfI6whF_0ChWLN4keYpA7uJhu68U9hvxRxVMIJVbtdSTDZx6QuVI6S3PvtXJMohXPwNP76rXpoWuVY-M65gk9dxcKr4Bc_t84y05yJa-POR1zQ_CT28HGF1QNjWWhiBnKLHcXEUEqM9HInEzcsdSpjIfUofsHQBjAuvLk-lLfSd8MArwwPprwSTpK46bIPw/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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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.*

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQ... 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/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... < https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWe... .

External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below antsRegistration --version

If it is below 2.1.0 download the 2.1.0 binaries here, it works for me. https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpU...

If you want to use your script, edit the yellow lines to remove "#" # If you want to build a particular release, do so here # cd ANTs # git checkout v2.3.1 # cd -

# If you want to build a particular release, do so here cd ANTs git checkout v2.3.1 cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis alandarkenergy@gmail.com wrote:

    External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu kingwai.chu@gmail.com wrote:

...

    External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis alandarkenergy@gmail.com wrote:

...

    External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found. Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the *antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis alandarkenergy@gmail.com wrote:

...

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 Caution

For 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:

...

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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 < 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 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.chu@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 < > alandarkenergy@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.chu@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-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 > > > -- > > *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* > > > > > *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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... > 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 *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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 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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... > 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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... > 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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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 > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... > 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 *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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 > <*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... > 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.*

---

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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... https://secure-web.cisco.com/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... https://secure-web.cisco.com/1kUg_dV0QxDtOWXilrxzAoM8AieGG16geE84CUkUAZzdBNmHrOjZZDtFeqUbxS5mjlbcxCHNpTRj01p9ynfe48PGFr7KvT2dMtVSPYyM4FQvClwqQv_NBRB5-d07oeTv2SibOzGSHo_8N4XXmVk022xGDfI6whF_0ChWLN4keYpA7uJhu68U9hvxRxVMIJVbtdSTDZx6QuVI6S3PvtXJMohXPwNP76rXpoWuVY-M65gk9dxcKr4Bc_t84y05yJa-POR1zQ_CT28HGF1QNjWWhiBnKLHcXEUEqM9HInEzcsdSpjIfUofsHQBjAuvLk-lLfSd8MArwwPprwSTpK46bIPw/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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.*

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... https://secure-web.cisco.com/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQfW9yxAcjT8r5jBuvrj9R7teuKjplAsGgG1hkDNCSrTcjOjMUIzgV7_Y_IOZb-BnLVs_YCLubjmTiCYNKInHuisZHsBJVfUP0m31LXco7gSa5EeukziGpJ_czSwSn-FeCNCdnAlKi7bra0ykrVwz28I7c_He6CuE1HdgodznPy_xVIqYe58X_VL7wchQshsbBAICzUuWzRGYFkcAxlaN9fciXK2iCth4TK888uKPJgMREgc_2Cq5WFo2mQ4tzjwJ2TxT7q_6QtnjVfbmETujuEyEi9Pxr85CTzc6T6Plg/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... https://secure-web.cisco.com/1FZTrEN5KcV4QB-2kn8RgF7ua0iNTOihf2JmdhixKie4ldqnOF1VGc2kE71NyESYP0ICpbljmkIXf8kmfX2AbD0MqmnXv6Mp4nt_JQcSY8TJQZgFSkSx_deD7QSfeeN1Q98BNIcVeH31rJsSHJzkSCjhKjy0v-C4KWtSl-T1lebx3akQnpAnqzmc-RAn_93gpDIljdkkSRyKL_TVc5b5KIHHjE8jibsBOUwYC8NxeB-ktV4V_47SG2KvUG9VSi6zi-4akqzV0PX0LIn0cA_Lp4Oqfqi5vVy84SpbUAxSqU8Bu3ApvxLRoeI9zp7lXO2b5gssNsoiGXdoBFc-hENz8MA/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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.*

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb4... 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/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... < https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld... .

External Email - Use Caution

Hi King Wai -

Thanks for your help. I downloaded version 2.1.0 as you suggested and installed it. But the error message keeps coming back. It is looking for this file:

/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh

But this file is not present in the binary folder.

Thanks,

Alan

On Mon, Aug 15, 2022 at 12:54 PM King-Wai Chu kingwai.chu@gmail.com wrote:

    External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below antsRegistration --version

If it is below 2.1.0 download the 2.1.0 binaries here, it works for me. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1aRj_2Cogi5eyd_6oSKBAHn9XqDXrW0S8mE6Ya3yHHveXzq... https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0

If you want to use your script, edit the yellow lines to remove "#" # If you want to build a particular release, do so here # cd ANTs # git checkout v2.3.1 # cd -

# If you want to build a particular release, do so here cd ANTs git checkout v2.3.1 cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis alandarkenergy@gmail.com wrote:

...

    External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu kingwai.chu@gmail.com wrote:

...

    External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis alandarkenergy@gmail.com wrote:

...

    External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found. Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the *antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis alandarkenergy@gmail.com wrote:

...

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 Caution

For 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 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 < > 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 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.chu@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 < >> alandarkenergy@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.chu@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-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 >> >> >> -- >> >> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* >> >> >> >> >> *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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... >> 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 *MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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 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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... >> 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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... >> 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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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 >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... >> 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 *MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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 >> <*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... >> 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.* > > > _______________________________________________ > 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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... > https://secure-web.cisco.com/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... > https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... > https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... https://secure-web.cisco.com/1kUg_dV0QxDtOWXilrxzAoM8AieGG16geE84CUkUAZzdBNmHrOjZZDtFeqUbxS5mjlbcxCHNpTRj01p9ynfe48PGFr7KvT2dMtVSPYyM4FQvClwqQv_NBRB5-d07oeTv2SibOzGSHo_8N4XXmVk022xGDfI6whF_0ChWLN4keYpA7uJhu68U9hvxRxVMIJVbtdSTDZx6QuVI6S3PvtXJMohXPwNP76rXpoWuVY-M65gk9dxcKr4Bc_t84y05yJa-POR1zQ_CT28HGF1QNjWWhiBnKLHcXEUEqM9HInEzcsdSpjIfUofsHQBjAuvLk-lLfSd8MArwwPprwSTpK46bIPw/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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.*

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... https://secure-web.cisco.com/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQfW9yxAcjT8r5jBuvrj9R7teuKjplAsGgG1hkDNCSrTcjOjMUIzgV7_Y_IOZb-BnLVs_YCLubjmTiCYNKInHuisZHsBJVfUP0m31LXco7gSa5EeukziGpJ_czSwSn-FeCNCdnAlKi7bra0ykrVwz28I7c_He6CuE1HdgodznPy_xVIqYe58X_VL7wchQshsbBAICzUuWzRGYFkcAxlaN9fciXK2iCth4TK888uKPJgMREgc_2Cq5WFo2mQ4tzjwJ2TxT7q_6QtnjVfbmETujuEyEi9Pxr85CTzc6T6Plg/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... https://secure-web.cisco.com/1FZTrEN5KcV4QB-2kn8RgF7ua0iNTOihf2JmdhixKie4ldqnOF1VGc2kE71NyESYP0ICpbljmkIXf8kmfX2AbD0MqmnXv6Mp4nt_JQcSY8TJQZgFSkSx_deD7QSfeeN1Q98BNIcVeH31rJsSHJzkSCjhKjy0v-C4KWtSl-T1lebx3akQnpAnqzmc-RAn_93gpDIljdkkSRyKL_TVc5b5KIHHjE8jibsBOUwYC8NxeB-ktV4V_47SG2KvUG9VSi6zi-4akqzV0PX0LIn0cA_Lp4Oqfqi5vVy84SpbUAxSqU8Bu3ApvxLRoeI9zp7lXO2b5gssNsoiGXdoBFc-hENz8MA/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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.*

---

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/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... https://secure-web.cisco.com/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb40_cYnHVm3ePaG2Q2CAAUPw7GOkx3N-9zCGSW0Dc1XqgFusNpSGmfA_bQcfhyW6_OrMFxNhb-OQ1YF9VHLAaoIDa7K8L-VV6Z1T5bmQQkflY3iYGSGy_Kjsuj1VsQgjy784uG7_UR9atmEhqYuz8lk1BWKFX5ENPpSpPv2ijp40x8ENr-fJZ-CCrSOZiAIXSyjkIKcaEuARlKsAeRavgDdEHK9fHLnyNgQXPVA7Pmb6k_Kaq2T4VOm5oFgrBiQKqh20ZLYUYt4wxD5kZeZM/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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 https://secure-web.cisco.com/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8... 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/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... < https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMp... .

External Email - Use Caution

Thank you King Wai and Philip. I am reworking the config file to see if that works. The earlier Tracula versions were much easier to run.

best,

Alan

On Mon, Aug 15, 2022 at 3:15 PM King-Wai Chu kingwai.chu@gmail.com wrote:

    External Email - Use Caution

Hi Alan,

Check the ANTs version. If you are using the binaries version 2.1.0 "antsRegistration --version" should return All_Command_lines_OK ANTs Version: 2.1.0-g78931 Compiled: Jan 23 2015 03:27:59

If not, you are not using the version 2.1.0

Do you know where is the binaries? You need to change ANTSPATH to point to the binaries.

Or open a new terminal and try again.

Best,

King-Wai

On Mon, Aug 15, 2022 at 3:46 PM Alan Francis alandarkenergy@gmail.com wrote:

...

    External Email - Use Caution

Hi King Wai -

Thanks for your help. I downloaded version 2.1.0 as you suggested and installed it. But the error message keeps coming back. It is looking for this file:

/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh

But this file is not present in the binary folder.

Thanks,

Alan

On Mon, Aug 15, 2022 at 12:54 PM King-Wai Chu kingwai.chu@gmail.com wrote:

...

    External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below antsRegistration --version

If it is below 2.1.0 download the 2.1.0 binaries here, it works for me. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/13dKtDNhInNLuuGRu_cvIWq471EtbnN8DrW6AxeabHhrJXv... https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0

If you want to use your script, edit the yellow lines to remove "#" # If you want to build a particular release, do so here # cd ANTs # git checkout v2.3.1 # cd -

# If you want to build a particular release, do so here cd ANTs git checkout v2.3.1 cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis alandarkenergy@gmail.com wrote:

...

    External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu kingwai.chu@gmail.com wrote:

...

    External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis < alandarkenergy@gmail.com> wrote:

...

    External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found. Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the *antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis < alandarkenergy@gmail.com> wrote:

> 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 Caution >> >> For 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 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 < >>> 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 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.chu@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 < >>>> alandarkenergy@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.chu@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-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 >>>> >>>> >>>> -- >>>> >>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* >>>> >>>> >>>> >>>> >>>> *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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >>>> 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 *MailScanner has detected >>>> a possible fraud attempt from "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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 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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >>>> 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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >>>> 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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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 >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >>>> 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 *MailScanner has detected >>>> a possible fraud attempt from "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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 >>>> <*MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>>> 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.* >>> >>> >>> _______________________________________________ >>> 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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >>> https://secure-web.cisco.com/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>> https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >>> https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... >> https://secure-web.cisco.com/1kUg_dV0QxDtOWXilrxzAoM8AieGG16geE84CUkUAZzdBNmHrOjZZDtFeqUbxS5mjlbcxCHNpTRj01p9ynfe48PGFr7KvT2dMtVSPYyM4FQvClwqQv_NBRB5-d07oeTv2SibOzGSHo_8N4XXmVk022xGDfI6whF_0ChWLN4keYpA7uJhu68U9hvxRxVMIJVbtdSTDZx6QuVI6S3PvtXJMohXPwNP76rXpoWuVY-M65gk9dxcKr4Bc_t84y05yJa-POR1zQ_CT28HGF1QNjWWhiBnKLHcXEUEqM9HInEzcsdSpjIfUofsHQBjAuvLk-lLfSd8MArwwPprwSTpK46bIPw/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >> https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... >> https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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.* > > >

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

*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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... https://secure-web.cisco.com/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQfW9yxAcjT8r5jBuvrj9R7teuKjplAsGgG1hkDNCSrTcjOjMUIzgV7_Y_IOZb-BnLVs_YCLubjmTiCYNKInHuisZHsBJVfUP0m31LXco7gSa5EeukziGpJ_czSwSn-FeCNCdnAlKi7bra0ykrVwz28I7c_He6CuE1HdgodznPy_xVIqYe58X_VL7wchQshsbBAICzUuWzRGYFkcAxlaN9fciXK2iCth4TK888uKPJgMREgc_2Cq5WFo2mQ4tzjwJ2TxT7q_6QtnjVfbmETujuEyEi9Pxr85CTzc6T6Plg/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... https://secure-web.cisco.com/1FZTrEN5KcV4QB-2kn8RgF7ua0iNTOihf2JmdhixKie4ldqnOF1VGc2kE71NyESYP0ICpbljmkIXf8kmfX2AbD0MqmnXv6Mp4nt_JQcSY8TJQZgFSkSx_deD7QSfeeN1Q98BNIcVeH31rJsSHJzkSCjhKjy0v-C4KWtSl-T1lebx3akQnpAnqzmc-RAn_93gpDIljdkkSRyKL_TVc5b5KIHHjE8jibsBOUwYC8NxeB-ktV4V_47SG2KvUG9VSi6zi-4akqzV0PX0LIn0cA_Lp4Oqfqi5vVy84SpbUAxSqU8Bu3ApvxLRoeI9zp7lXO2b5gssNsoiGXdoBFc-hENz8MA/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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.*

---

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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... https://secure-web.cisco.com/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb40_cYnHVm3ePaG2Q2CAAUPw7GOkx3N-9zCGSW0Dc1XqgFusNpSGmfA_bQcfhyW6_OrMFxNhb-OQ1YF9VHLAaoIDa7K8L-VV6Z1T5bmQQkflY3iYGSGy_Kjsuj1VsQgjy784uG7_UR9atmEhqYuz8lk1BWKFX5ENPpSpPv2ijp40x8ENr-fJZ-CCrSOZiAIXSyjkIKcaEuARlKsAeRavgDdEHK9fHLnyNgQXPVA7Pmb6k_Kaq2T4VOm5oFgrBiQKqh20ZLYUYt4wxD5kZeZM/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... https://secure-web.cisco.com/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8p_kJk5tVNUx8jDj0llLwX7uB0U06oO3UjTAhlFu7fhIPO0BLislGWGR8IoFSqLy2ifItJc6FndvwwQWTvfOQZLKELW0-DAtPgqJ2RjgqMbxz3eJO6_hg7D-2dbzxPT_E_hJBukixxaN2nG8GlCIhQMZoO_3ZKWD7qw-ey_F3Ersc8x9H_tj_1XEFALrNE4EixYbX9BqUtLY3CVZC3gSIjLds7Itc3ms0cWrtJZIvS6Uc8jvAXM62wsgkPBTM08UX6xzjzZ-sJOwtclUZMpahtROa7keQpkAmEo_55wDw/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMpBAgD5IP-MBX_o_DJkQOTWjx8bp2DX36buvN0WClPue4wHivnOSXoyjA3nGIVL85F5c9xueKcqfmZIpIZNLpLFkCSqHzbvXtaE_RsZjiSTGoALv1GHCLeucaC139vRFGw26TZ35aJTTRUUKXU2XVJTLrHnE02t8Fc8mxvr4tHOwJBi0QuAjPqw9OUJkGli5WDRcyI7OiRIt85FeUtz0zMjkHFG0v-h5UvneRJCeOtTwUkW4a3RDiHhkqtyeB1p83ULDEf4fQWIhAjwHY2OsQkq7-0pvAJMz3YH1RL1__Q/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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMpBAgD5IP-MBX_o_DJkQOTWjx8bp2DX36buvN0WClPue4wHivnOSXoyjA3nGIVL85F5c9xueKcqfmZIpIZNLpLFkCSqHzbvXtaE_RsZjiSTGoALv1GHCLeucaC139vRFGw26TZ35aJTTRUUKXU2XVJTLrHnE02t8Fc8mxvr4tHOwJBi0QuAjPqw9OUJkGli5WDRcyI7OiRIt85FeUtz0zMjkHFG0v-h5UvneRJCeOtTwUkW4a3RDiHhkqtyeB1p83ULDEf4fQWIhAjwHY2OsQkq7-0pvAJMz3YH1RL1__Q/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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-- 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/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ... 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/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... < https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY... .

External Email - Use Caution

Thanks Anastasia.

On Thu, Aug 18, 2022 at 1:04 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

Earlier versions of TRACULA didn't have the option to use ANTs for registration. Now you have that option, but you also have the option not to use it, if you're finding it hard to install.

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Wednesday, August 17, 2022 4:46 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Tracula - Preproc

    External Email - Use Caution

Thank you King Wai and Philip. I am reworking the config file to see if that works. The earlier Tracula versions were much easier to run.

best,

Alan

On Mon, Aug 15, 2022 at 3:15 PM King-Wai Chu kingwai.chu@gmail.com wrote:

    External Email - Use Caution

Hi Alan,

Check the ANTs version. If you are using the binaries version 2.1.0 "antsRegistration --version" should return All_Command_lines_OK ANTs Version: 2.1.0-g78931 Compiled: Jan 23 2015 03:27:59

If not, you are not using the version 2.1.0

Do you know where is the binaries? You need to change ANTSPATH to point to the binaries.

Or open a new terminal and try again.

Best,

King-Wai

On Mon, Aug 15, 2022 at 3:46 PM Alan Francis alandarkenergy@gmail.com wrote:

    External Email - Use Caution

Hi King Wai -

Thanks for your help. I downloaded version 2.1.0 as you suggested and installed it. But the error message keeps coming back. It is looking for this file:

/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh

But this file is not present in the binary folder.

Thanks,

Alan

On Mon, Aug 15, 2022 at 12:54 PM King-Wai Chu kingwai.chu@gmail.com wrote:

    External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below antsRegistration --version

If it is below 2.1.0 download the 2.1.0 binaries here, it works for me. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1btFY3Fi2MO01giADcDsg_LuZt2gZ5wSC16du2oDTOCRItS... https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0

If you want to use your script, edit the yellow lines to remove "#" # If you want to build a particular release, do so here # cd ANTs # git checkout v2.3.1 # cd -

# If you want to build a particular release, do so here cd ANTs git checkout v2.3.1 cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis alandarkenergy@gmail.com wrote:

    External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu kingwai.chu@gmail.com wrote:

    External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs? It should be 2.1.0 Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis alandarkenergy@gmail.com wrote:

    External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022 /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found. Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the *antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis alandarkenergy@gmail.com wrote:

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 Caution

For 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 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 < 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.

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*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 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.chu@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 alandarkenergy@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.chu@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-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.*

---

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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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 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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... 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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... 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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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 <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... 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 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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1bpeq-EpVr7xC-LfhZp68OO27V1EnvYoE13U_m2UuuTN-MU4a75ULXavmGrUMnj-vey0neBueNM0l0QS9OlE-4ZIEA77TGwuOdKsAE-iyJnsUurdVbCH-81kMeRrT4e-ojvworVjEraq7xO7QwRnsBNriudwdUZeIGXfxiRlw27HUSJC5d5MRH5KfLTAFvfszCNJEOEWDDMSrJtyCwTcA_2h_uZeIgMdXAf691m4GfZ_lt7UFPQ7vrKOGNw757Al5_g-UogL9BtjdUxp7lO4gTAI059niVqtiCIioqkwHUd1RGLCNU0Lf-3N-nWApjVeq/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1x4HJwDlBKI2bhG9GRQtnXU5WC24mFqyrzIRbkP_Ng1JkZ3MfFGHAaZuQeTJ_ZfAIoGkbRPGTx6GicQjV35UMGJBTnZ2z8Mwf3jjimcaBU-eWIPnLEKQZvPinzyPsIOeAUD5CopkjB1--id_r0KC1zJbICdwAOutOsxOhmjQPKqlu6xy4SINbceY0DmQQD-j3UvG3ttnta9Bm254_0LL0KL5yLmuH1D_NeSLdttc5Qt0viVlxkQ59DDUkTXBWkewY0qARO8J1ci6NPmX2R7F1MO8H3uZOxzdHGFCBxWiwTd2n-D_-pq1l30X5rIoWKXRk/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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1kUg_dV0QxDtOWXilrxzAoM8AieGG16geE84CUkUAZzdBNmHrOjZZDtFeqUbxS5mjlbcxCHNpTRj01p9ynfe48PGFr7KvT2dMtVSPYyM4FQvClwqQv_NBRB5-d07oeTv2SibOzGSHo_8N4XXmVk022xGDfI6whF_0ChWLN4keYpA7uJhu68U9hvxRxVMIJVbtdSTDZx6QuVI6S3PvtXJMohXPwNP76rXpoWuVY-M65gk9dxcKr4Bc_t84y05yJa-POR1zQ_CT28HGF1QNjWWhiBnKLHcXEUEqM9HInEzcsdSpjIfUofsHQBjAuvLk-lLfSd8MArwwPprwSTpK46bIPw/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1GL03L1l_QTysUr7QDilnJ3aIzwH_EvMQM8Zv8pmLs31ZBPistWhabOm1qlazRdQ--ufU7ZOuAgZd1AyasC2iPok_PBaJc4euhQPmMecZGSb6mpc5ayoDinsxdUTFjDU2_KF7K347PAvTd08gx2NVDvGe8bGffGLVLwelYIIXlJgokNEvb3j1LroJl9hHpcmmT5QVUt8QaR_KvjaQwl-BQuhYV5PEwqEjUB0lYE2Hggm7QFf4X49ZzNkQOaHKxLqCrFZQhECSKVAAoG4WaRopyPIIOF2kZ-vNKQYhRiqwgLCekiaw2yxzsDesl8lElwEMeXaKgM1-rCh0C2UoK_Altg/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. *

-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*

• 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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1XH3S9mn0TJRoB2RWedFAogV22-Sq0FrSD11Pqegx8kYzyQfW9yxAcjT8r5jBuvrj9R7teuKjplAsGgG1hkDNCSrTcjOjMUIzgV7_Y_IOZb-BnLVs_YCLubjmTiCYNKInHuisZHsBJVfUP0m31LXco7gSa5EeukziGpJ_czSwSn-FeCNCdnAlKi7bra0ykrVwz28I7c_He6CuE1HdgodznPy_xVIqYe58X_VL7wchQshsbBAICzUuWzRGYFkcAxlaN9fciXK2iCth4TK888uKPJgMREgc_2Cq5WFo2mQ4tzjwJ2TxT7q_6QtnjVfbmETujuEyEi9Pxr85CTzc6T6Plg/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1-8oOkK-wLPMrAmkNjkFEXX-S2C0Q9yvT36t1o2AMLHEmWejdtngiYJ0ZvHXcXHZrlzGiromD9lRhTimzetDBMDCr1FPaomAXT7Xlfm24YxcKSGgkoqjl1YkYkfIMLuUvwKFnhlnNJjKC1GRrUTysnazzYWdeqcDi1G41vWPSpgYDSxa9GGxvjkElvM6Hd1_iDMy9D51TxV8aFPZhYJ76gb5gbj_JnwoNVby4VCTpVn-WcQ-ObZFZ6vWRGkupddXhMWnQPM3Qoucu8WTnnOzn2r4Mpyhn1fYZEpFCS78Bf-lsQGb-6unsYA8jxAJMEPPa2pOESOxSO9piMYCia4cKwg/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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1FZTrEN5KcV4QB-2kn8RgF7ua0iNTOihf2JmdhixKie4ldqnOF1VGc2kE71NyESYP0ICpbljmkIXf8kmfX2AbD0MqmnXv6Mp4nt_JQcSY8TJQZgFSkSx_deD7QSfeeN1Q98BNIcVeH31rJsSHJzkSCjhKjy0v-C4KWtSl-T1lebx3akQnpAnqzmc-RAn_93gpDIljdkkSRyKL_TVc5b5KIHHjE8jibsBOUwYC8NxeB-ktV4V_47SG2KvUG9VSi6zi-4akqzV0PX0LIn0cA_Lp4Oqfqi5vVy84SpbUAxSqU8Bu3ApvxLRoeI9zp7lXO2b5gssNsoiGXdoBFc-hENz8MA/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1C98EGcFMaOxg0iR7RWGrv7MsnftXuOVKY5JppzmzD2fKx83TWixyLI6pqQ1ZS3ZYBj2nz4O8QbB-xH1JloG3Bm5bNyAL6aU9JMrwwwtg09NVmkHNiCCeH2LQBg6MLIjJ5bjNmI2WSzTTfAjqR5p4gxWnYFxSC0PsWwVHmaJ65Ixb3MjMJPdihiSz9ztIxDrsAaX6wq2jHw3D4gsVoRA1kqf6QlgmipCDCVxlX2_T2zlIa4cA61IrOF14Vy_yqQ5DjPVyw-y25Cip2lATh2i1RrXR1dSnwoUVuPpTRGVJ1XR-1yjTaoalNI8YuR9dS4aenwRosqRw8YZZykG4rzwyHg/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1G8t_LBqckS2rU7MJO3PZuydB3WlH-1PzMbmLgDLeFeCLb40_cYnHVm3ePaG2Q2CAAUPw7GOkx3N-9zCGSW0Dc1XqgFusNpSGmfA_bQcfhyW6_OrMFxNhb-OQ1YF9VHLAaoIDa7K8L-VV6Z1T5bmQQkflY3iYGSGy_Kjsuj1VsQgjy784uG7_UR9atmEhqYuz8lk1BWKFX5ENPpSpPv2ijp40x8ENr-fJZ-CCrSOZiAIXSyjkIKcaEuARlKsAeRavgDdEHK9fHLnyNgQXPVA7Pmb6k_Kaq2T4VOm5oFgrBiQKqh20ZLYUYt4wxD5kZeZM/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/172-UOQhlCXRtQPjexvHx3hpn76JuMAR5aYSXn2GAiNxlld2QN0D2CPKtV7Sw5jCxBf0lVGuhbq0xrbXRyG33QP6y6ueO0BNVIXTYKjWng6r22NQgKztOiUNLoVblop14lx6s4Twe_xq9_HBjzBgoSAGPdnP2Icr2ozPjnNFJDcvUt8TpnQGbZWWguFAZu1NgJaaITHWrwfeZ96qHMCOYmZHXhH7sVR676gDNCl3o7YOt3xAnY37uLLnrTSSqkRJpv5JQdGK3_ZPHlLaLLuMs3xnfB_sOpgFabhfYzMo0302uBKa-EAvzAGJlK390IHeQ/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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1xicjt929zRi2I8xu7JZUV64PqLL-rDg3kp2bYn4udxK5c8p_kJk5tVNUx8jDj0llLwX7uB0U06oO3UjTAhlFu7fhIPO0BLislGWGR8IoFSqLy2ifItJc6FndvwwQWTvfOQZLKELW0-DAtPgqJ2RjgqMbxz3eJO6_hg7D-2dbzxPT_E_hJBukixxaN2nG8GlCIhQMZoO_3ZKWD7qw-ey_F3Ersc8x9H_tj_1XEFALrNE4EixYbX9BqUtLY3CVZC3gSIjLds7Itc3ms0cWrtJZIvS6Uc8jvAXM62wsgkPBTM08UX6xzjzZ-sJOwtclUZMpahtROa7keQpkAmEo_55wDw/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMpBAgD5IP-MBX_o_DJkQOTWjx8bp2DX36buvN0WClPue4wHivnOSXoyjA3nGIVL85F5c9xueKcqfmZIpIZNLpLFkCSqHzbvXtaE_RsZjiSTGoALv1GHCLeucaC139vRFGw26TZ35aJTTRUUKXU2XVJTLrHnE02t8Fc8mxvr4tHOwJBi0QuAjPqw9OUJkGli5WDRcyI7OiRIt85FeUtz0zMjkHFG0v-h5UvneRJCeOtTwUkW4a3RDiHhkqtyeB1p83ULDEf4fQWIhAjwHY2OsQkq7-0pvAJMz3YH1RL1__Q/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/1iIB2QVqzDotPbUezfziepNnnPIj-cTrG4e-9P7pKfNefMpBAgD5IP-MBX_o_DJkQOTWjx8bp2DX36buvN0WClPue4wHivnOSXoyjA3nGIVL85F5c9xueKcqfmZIpIZNLpLFkCSqHzbvXtaE_RsZjiSTGoALv1GHCLeucaC139vRFGw26TZ35aJTTRUUKXU2XVJTLrHnE02t8Fc8mxvr4tHOwJBi0QuAjPqw9OUJkGli5WDRcyI7OiRIt85FeUtz0zMjkHFG0v-h5UvneRJCeOtTwUkW4a3RDiHhkqtyeB1p83ULDEf4fQWIhAjwHY2OsQkq7-0pvAJMz3YH1RL1__Q/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1ay6yLL-GhbhkV5RNJEjED_OwejF5ANJkDDjuOR-IxTnROsxgnL2ZfvneHVVf_t_S79VgGsOWwU0nqJSHT3ge5UVUFD-KcxF3Sh38WJbgmmU_VeDF782nGlJea7rUhLxfw6A-EKW-pc2hVwrqcMgyOtR-8_TyK0qt7uzsKn0jWdMpl1hKhvPDG7quC0iFv3CxSFk96FG9fO0EBdRfcAHU-Uup6Xyp_PgZSlp_Zrn43o7KEgFROj9rUqMexxvGLeO2gSXsfRvtSoA1c8IPcrsowkzLBM1EDccPxpUHbozMZuSslwiYwy8lOKxvYHRBDORw09C6C47vr9KKekmaGEW1zg/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/17dDDoEZG1pwztS9Keaa7CLtl-wwiIoakLA3d9XGs1YedLExEDO1z0sgEXwMQZFc0Qd7ycMBeDZK1e-rztkcikL-Ydg98Bs5kh2FhF1O-biUeAhVdC7tOQxIyIfMGQTBZAIo_jv6J7g4GLbuRbgD2-mGLtinN4Ps93aCNrnpEV9mL4LR7oawLXIMUWSfOd-vg3qL7je72Mt41tPkFWXb-zK4Dv91XeLtAHRKUZ7q-WDcbDx7Yjmmw4QFLLURFS4NBJVAH40zH7BiVjAn7Y0bg-Nr6JS880SPdCeBXly4-HNJBjVeuKcSU2dD92GkiI6SqF2et1JdQitkjrJQEE379Lw/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/17dDDoEZG1pwztS9Keaa7CLtl-wwiIoakLA3d9XGs1YedLExEDO1z0sgEXwMQZFc0Qd7ycMBeDZK1e-rztkcikL-Ydg98Bs5kh2FhF1O-biUeAhVdC7tOQxIyIfMGQTBZAIo_jv6J7g4GLbuRbgD2-mGLtinN4Ps93aCNrnpEV9mL4LR7oawLXIMUWSfOd-vg3qL7je72Mt41tPkFWXb-zK4Dv91XeLtAHRKUZ7q-WDcbDx7Yjmmw4QFLLURFS4NBJVAH40zH7BiVjAn7Y0bg-Nr6JS880SPdCeBXly4-HNJBjVeuKcSU2dD92GkiI6SqF2et1JdQitkjrJQEE379Lw/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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... https://secure-web.cisco.com/1LYyn2046cKwb_dtdKo1fGfCeF2cCHJZLlDR3T5CIkhwiUQ4rmq405pUUPQztVGltF1QdldT2Z0OfFORI-9i5pfgkU_BYkDWrLOAMWAt1TcfdvDNRjiizPCPNEXlS9Mjbl64ee4AGC1ox-7RLQ1ltsWckNGuk5tCtow0xQ5-2TePmGLyFhIO3ZMjgT9Vx7eOzaRkMUs3cMbbSHlqGbKs1_gOlksMsKU5j_49kDQJvUaRHP1oeZLUMoEciEjhtVC7dj7CIbu0-F0oupoHkhsI8fzsIbXTyWoFLU5Xb3069AbEWQ7M43ry0ikbaJzjVrhDE/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY8TvyCpyGIdvPDxoZSmNTepB4s6Toet7y5CSVuHM0OhtIurc-8ZZ9RUpFkkcWzwmZJv6e8rmsrVjyBukoGUT2NvbJ8EazWo6TTGJK50MaoBjgPbjjINooVS1b6xwnKKZT_N1G07ziuPY5JY0_YXIUZ276adq3ISydL7w0hEmcZrNMczc3BMrMwq45MHbr3qnzqf2y1sA6NqkEpvotGENW3jBwSPRgo7cs8VSMFUfUllP0YrvJvut8J-_B9_TLfUNE1dHPcuW2AmxXCYC3qx/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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... https://secure-web.cisco.com/14ECjSXLRxQQSPq0vFyc8JkkgC3zeXygx63pVeZl34XYuVY8TvyCpyGIdvPDxoZSmNTepB4s6Toet7y5CSVuHM0OhtIurc-8ZZ9RUpFkkcWzwmZJv6e8rmsrVjyBukoGUT2NvbJ8EazWo6TTGJK50MaoBjgPbjjINooVS1b6xwnKKZT_N1G07ziuPY5JY0_YXIUZ276adq3ISydL7w0hEmcZrNMczc3BMrMwq45MHbr3qnzqf2y1sA6NqkEpvotGENW3jBwSPRgo7cs8VSMFUfUllP0YrvJvut8J-_B9_TLfUNE1dHPcuW2AmxXCYC3qx/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/1C-FrMEzruLmqp-dTZoYAHPYz_ONGvJ0ale-dvKdVZ2Ihza... 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/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... < https://secure-web.cisco.com/1-xQANi5tXx1u-NeMq-BWgz5AX6mtCulk3DqabtZw_LwmFd... .