External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are a lot of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis alandarkenergy@gmail.com Sent: Thursday, August 4, 2022 12:23 PM To: Freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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 -
Thank you so much. I will do as you suggested.
best wishes
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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 https://secure-web.cisco.com/1rnwhqaAvrjIPhTTZ-jS08gtbsEm8Zz0bOLdaaH5aEKGgEP... 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/1Y94zrR_0sElA34xaZV95EmcQjtEksdDNW-gZ7Bw651WluR... < https://secure-web.cisco.com/1Y94zrR_0sElA34xaZV95EmcQjtEksdDNW-gZ7Bw651WluR... .
External Email - Use Caution
Good morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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 https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_Mc... 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/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PX... < https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PX... .
External Email - Use Caution
Hi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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/147r4yKWXDa0ksyQ_uy68dtWkcYD3-JmqjORDjb8wn1yq_r... https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/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/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl... https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl... https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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/147r4yKWXDa0ksyQ_uy68dtWkcYD3-JmqjORDjb8wn1yq_r... 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/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl... < https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl... .
External Email - Use Caution
Thank you King-Wai.
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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/19VhWc0-IQ2-vY6VvZ_Xa-9akD2Cd1BClFs7YJo3ZLQw2n7... https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/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/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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/19VhWc0-IQ2-vY6VvZ_Xa-9akD2Cd1BClFs7YJo3ZLQw2n7... https://secure-web.cisco.com/147r4yKWXDa0ksyQ_uy68dtWkcYD3-JmqjORDjb8wn1yq_rsrwgA_BsryMv4A4tG4MDuknwm94cEnJDZbHhKopKetiFD1jOAz8LydOql5U6nIxNQOmhIOpsL546Pz2jHWWcBaCjM9zwxc1v7wLO1YnJ0jwqPjYSuLPLnmU7ik9jKak1dH9olnDiywVCLo2Ki1ikF7Otbd1osYYzRZkuguuxYM8Vjt12MrHYJd34xLd4ZX2a8D7xCcJyH85YOqRe3Mh9k13cvwOa6elIfClYhwJmEeWNZXi2YLSgZHtIrSwwf8lIrX5PE_5CaDIZmPGIwm/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/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl86MlMfZaWHXtWQ_xvoSoFe19ETRJ0qeFiEx1Mb5d5yKdu6DBbnmZEJcOC5lR-T_11kBRKJX49sFd8PZcKE0FpVoqGN0-yej4ZPiOXCrL76SHzSJJeeIRhWzLGRkxsDbZIAzxCt4NMorpwX2wHW4YsfzLBVVJeBWw_9eyvedZ4NyJutBZuE8aV595Kp2f8I1v_dv3nbu4juE2mdORcvSqy3unc9oTm0a0dhj85ojssfTY7c2-tEPDUYpltXeCOuJ1WkNMDJCEj9YbkeW7V3/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/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl86MlMfZaWHXtWQ_xvoSoFe19ETRJ0qeFiEx1Mb5d5yKdu6DBbnmZEJcOC5lR-T_11kBRKJX49sFd8PZcKE0FpVoqGN0-yej4ZPiOXCrL76SHzSJJeeIRhWzLGRkxsDbZIAzxCt4NMorpwX2wHW4YsfzLBVVJeBWw_9eyvedZ4NyJutBZuE8aV595Kp2f8I1v_dv3nbu4juE2mdORcvSqy3unc9oTm0a0dhj85ojssfTY7c2-tEPDUYpltXeCOuJ1WkNMDJCEj9YbkeW7V3/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/19VhWc0-IQ2-vY6VvZ_Xa-9akD2Cd1BClFs7YJo3ZLQw2n7... 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/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... < https://secure-web.cisco.com/1bubUf1H7-r9zvR4uSWCJtlxFGmJVSwjP5N-QaD032iuPim... .
External Email - Use Caution
Hello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af rh.af lh.ar rh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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 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/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgte... 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/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A4... < https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A4... .
External Email - Use Caution
Hi Alan,
They still don't match. See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.af http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.ar http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.ar http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/11covYpNG9XogCXNSKkEfQ4sHz7Fzi5j-cYHWmfjoP40VT5... https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1bAhXd1A4Kld4wu9TbJwNaaj9jEK3Lc5xXttd8bTuqFMOKy... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1bAhXd1A4Kld4wu9TbJwNaaj9jEK3Lc5xXttd8bTuqFMOKy... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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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External Email - Use Caution
Hi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file. I made the changes that you suggested, but the error keeps coming up.
I have attached the file.
Thanks again,
Alan
On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
They still don't match. See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.af http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.ar http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.ar http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
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- Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley *
*Texas. *
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*Alan N. Francis 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Nj... https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIc... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIc... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Nj... 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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIc... < https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIc... .
External Email - Use Caution
Hi Alan,
In your pathlist, the 1st path is acomm. You have "ac" in your file. Change ac to acomm and you should be good to go.
Best,
King-Wai
On Fri, Aug 5, 2022 at 4:23 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file. I made the changes that you suggested, but the error keeps coming up.
I have attached the file.
Thanks again,
Alan
On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
They still don't match. See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.af http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.ar http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.ar http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1XlCWn3g7bLYkF8PVtxFGc9r5F-BB3nFMLFsiBFhEvLPv48... https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley*
*Texas.*
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-- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1XlCWn3g7bLYkF8PVtxFGc9r5F-BB3nFMLFsiBFhEvLPv48... https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/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/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/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/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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*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/1XlCWn3g7bLYkF8PVtxFGc9r5F-BB3nFMLFsiBFhEvLPv48... 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/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... < https://secure-web.cisco.com/1aHMYfdxRtrh8F2Y8pmgwBUb3rWopFj-jT8KbDBICp5_syp... .
You only need to specify path names if you don't want to reconstruct all 42 paths. But from the list, it looks like you want all 42 paths, so you don't need to specify anything. Skip all of those lines and you'll get the default behavior. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of King-Wai Chu kingwai.chu@gmail.com Sent: Friday, August 5, 2022 5:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula Config file.
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Hi Alan,
In your pathlist, the 1st path is acomm. You have "ac" in your file. Change ac to acomm and you should be good to go.
Best,
King-Wai
On Fri, Aug 5, 2022 at 4:23 PM Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> wrote:
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Hi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file. I made the changes that you suggested, but the error keeps coming up.
I have attached the file.
Thanks again,
Alan
On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> wrote:
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Hi Alan,
They still don't match. See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> wrote:
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Hello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.afhttp://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.afhttp://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.arhttp://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.arhttp://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> wrote:
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Hi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> wrote:
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Good morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are a lot of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
________________________________ 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 4, 2022 12:23 PM To: Freesurfer <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula Config file.
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Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
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.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/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/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/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/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/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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-- 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.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/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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-- 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.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/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/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/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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-- 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
External Email - Use Caution
Thank you Anastasia and King-Wai.
On Fri, Aug 5, 2022 at 4:12 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
You only need to specify path names if you don't want to reconstruct all 42 paths. But from the list, it looks like you want all 42 paths, so you don't need to specify anything. Skip all of those lines and you'll get the default behavior.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of King-Wai Chu < kingwai.chu@gmail.com> *Sent:* Friday, August 5, 2022 5:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Tracula Config file.
External Email - Use CautionHi Alan,
In your pathlist, the 1st path is acomm. You have "ac" in your file. Change ac to acomm and you should be good to go.
Best,
King-Wai
On Fri, Aug 5, 2022 at 4:23 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file. I made the changes that you suggested, but the error keeps coming up.
I have attached the file.
Thanks again,
Alan
On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
They still don't match. See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionHello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.af http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.ar http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.ar http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu kingwai.chu@gmail.com wrote:
External Email - Use CautionHi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis alandarkenergy@gmail.com wrote:
External Email - Use CautionGood morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are *a lot *of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Thursday, August 4, 2022 12:23 PM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula Config file.
External Email - Use CautionHi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
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- Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley *
*Texas. *
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- Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
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*Rio Grande Valley *
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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/1zFWI-vt2-94hiqwkc9ZKcNYJrMsn4RhyqnRC6FcllwInbu... https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... https://secure-web.cisco.com/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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- Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
Neuroscience* *University of Texas, School of Medicine*
*Rio Grande Valley *
*Texas. *
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-- 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/1zFWI-vt2-94hiqwkc9ZKcNYJrMsn4RhyqnRC6FcllwInbu... https://secure-web.cisco.com/1zY1g2on5YQ3Gv0NNc07RZJvcgHUNLpwAJ3H5-CiesJ-5Njoi7IEFJx9C96F5Cr31bH9sjoRyCm90AG8SGMHMJ1v-PUzr5489DbaI-2NdzarARQqVSxVk_u0bjCcZsMZa05deu7PopqLnLPPRxNwF6X51TZeT3hP-mATPH8OIUsA1uM5m3v3yZacO0l4JY8WPUX-JBRFkNWJAYw7Qhm6qjqQWObKoj15Wstm4w08NMcYWE2wahVqcVHl6_UatSPfxvqi4MKMHp-g3Pm--927MuEqlEfgPMFruOEy3KuzEuWZWcE9DYePrj_6S7lAwkCUh6MX7qU0Av4D6E-IBr5y74A/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/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/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/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... https://secure-web.cisco.com/1FcxhvYzte4dL2y8sR2vAOf1_PHF_ZgFrqJN_U7g7ULQdIciiSyi0nRtqDc8HHvUdV4sncn3Jp9kWINDaQgap0npOtPFdMCSTYBevjM9UizGNbaU2QGeWxCG1I78bAnchmUqQpUkC1gF1zE3nFethAFfV0Ay-vstrxBCpB2C1DmkFnB01NvLp7QwQV-rVieI7NYHNiLdWbIwyxqMw-tfn_mEA_cjlz106uW6oh2KPvsiIkIr6FAdEv4XcZ_i2bg3nJ65cqUbDAuCmMMslolxBmo5fPiZJYwZPuan04jFKd7JGNZviWA596fBy42niwHrOZLqYcABOBqfj2lMjpyjxNg/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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-- 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/1zFWI-vt2-94hiqwkc9ZKcNYJrMsn4RhyqnRC6FcllwInbu... 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/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... < https://secure-web.cisco.com/1VThazplF4oNYuDwG-RngDk1WJJzO4ont4kY3yogX61BnU5... .
You don't need all that stuff. You should remove everything below the bvalfile line and use the default parameters. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis alandarkenergy@gmail.com Sent: Friday, August 5, 2022 2:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula Config file.
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Hello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.afhttp://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af rh.afhttp://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af lh.arhttp://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar rh.arhttp://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> wrote:
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Hi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match. You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> wrote:
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Good morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect:
set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist = (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are a lot of things that you left in there from the example RC file. You should delete them entirely, unless you specifically want to set one of those things to something other than the default. These are examples that may not give you the default behavior. Also the field mapping files - delete those lines because you're just using the example names and they're not going to work. You want your RC file to have the minimum necessary for your analysis.
Best, Anastasia.
________________________________ 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 4, 2022 12:23 PM To: Freesurfer <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula Config file.
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Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
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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.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/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/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/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/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/1Mo_3lpp1WYcDiJ1Px2YSmOR_VRv9e6X5iFj2XdDtFZt2A47RRrBdECDhYLOMUMGjgKwQXMlVe3vDU25fIrIRPLXFvxvt86Ci3acCjwaDx9bqmk3MDSqVNgAAYGyB7eIbtkqChfXTTVmU6OM6tTDejK4UhhQE9kuut0ToKhni0FISTuVfySSD9MAvAS8vVzqjRAt35jXQpoV9iNKhmhRNH1HmbPl36Ssa6PNb8bxYPmBqaFlCGA33y0_v61XokdgBCg6y-iRPp45GfllrK4mTA6UECAsXwV500Lqt28pmfRizHF1wMwpTnoT_0QvSLN479QhkKoXufGTK1zScfUGbdA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Alan N. Francis PhD Assistant Professor of Neuroscience Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley Texas.
freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
King-Wai Chu -
Yendiki, Anastasia