External Email - Use Caution
Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using?
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0-beta/
Let us know how it goes! 🙂
Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com Sent: Sunday, July 18, 2021 2:18 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use Caution
Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using?
External Email - Use Caution
Hi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them. - During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist). - trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty...), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvG...
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8... 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 http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0Gm... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com Sent: Tuesday, July 20, 2021 2:17 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use Caution
Hi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
* I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them. * During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist). * trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0-beta/https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Sunday, July 18, 2021 2:18 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use Caution
Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
I used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Tuesday, July 20, 2021 2:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence,
thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
- During trac-all -prep there were errors of pathlist and trclist; it
was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
- trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1TZgoy19AfhMjwInlDd-P5_RLLijNVHwoesce4ZNdwZezMU... https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eJ3iTT7UJJyxyjlAJiSgYbe_2qtOlHo7gVC1Bsl0hIvNfu... https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/15pumBR0k2yUDnVLRQXHbamJjtKkhtAOwRY_gZg9xgRGpTf... https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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* http://secure-web.cisco.com/1p0I0MlPLP2kEVo1ksQYIBnuoxvNFaPTiAXjbNDd1Nc09_Yz... http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15pumBR0k2yUDnVLRQXHbamJjtKkhtAOwRY_gZg9xgRGpTf... 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 http://secure-web.cisco.com/1p0I0MlPLP2kEVo1ksQYIBnuoxvNFaPTiAXjbNDd1Nc09_Yz... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com Sent: Wednesday, July 21, 2021 2:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use Caution
I used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, 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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Tuesday, July 20, 2021 2:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use Caution
Hi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
* I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them. * During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist). * trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0-beta/https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Sunday, July 18, 2021 2:18 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ 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/15pumBR0k2yUDnVLRQXHbamJjtKkhtAOwRY_gZg9xgRGpTfAoFrv0QvlfC8XEntCh_LqVkxnOorujG_MK7xW2tym3k6rT2z_soL8mv12tCTF802YI75-IKLu2zokLgiBM3qOFFXz7oExbR9PUxvfIqwX8AfH5dAQbKSYTuPyfDsUAjNZoUE2aTiK2SvrM--a3c_XRgNVnMGkIq-PukmOVK1GEpxOZrF_e-T4JPlz943NyKwkkvn2d5cW31iWhnh1IpAFziLnhiv_e1A8-W2WmZA/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1p0I0MlPLP2kEVo1ksQYIBnuoxvNFaPTiAXjbNDd1Nc09_YzBN4f81rzz2FNNASj6fj_lB4mShJ0iAkGjJlacAQUSIoirOuw9pl2pXkrsC_w_1GtWWaGWGXtBRKU8HpRw6ddhsrxyxdB3roU2OFr1Q-U6UGiUimVKCEbJdZIzmuonuQhGNIu6fcAPdg0T7vll8arN5C1dr7U9InoGTVh-wZKUGZ9E7G-8ripFKLcUiOl7riHXup5e7cFpD_KkcOtMtavaFtkjjAVW048yfAQHPg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Thanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Wednesday, July 21, 2021 2:54 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionI used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Tuesday, July 20, 2021 2:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence,
thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
- During trac-all -prep there were errors of pathlist and trclist; it
was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
- trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1o5bTcN0JbJQRnx8FO0NDXchI7s97O1jeoXDDdIrYW6rmM9... https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1a0moWhkzbKbDKQgOYYTJzOSLF39tNfDAEnM3GJwmRKVEjI... https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/18_Xw5Gv3dqTB13zS_YEjzF-1Arlrr2M3gY3UHKXdqSWReR... https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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* http://secure-web.cisco.com/1euc3IZmziNkQEGPrbT3j3xXlUcAxPPaKWiZ0CYjU1kQqaDU... http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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/18_Xw5Gv3dqTB13zS_YEjzF-1Arlrr2M3gY3UHKXdqSWReR... https://secure-web.cisco.com/15pumBR0k2yUDnVLRQXHbamJjtKkhtAOwRY_gZg9xgRGpTfAoFrv0QvlfC8XEntCh_LqVkxnOorujG_MK7xW2tym3k6rT2z_soL8mv12tCTF802YI75-IKLu2zokLgiBM3qOFFXz7oExbR9PUxvfIqwX8AfH5dAQbKSYTuPyfDsUAjNZoUE2aTiK2SvrM--a3c_XRgNVnMGkIq-PukmOVK1GEpxOZrF_e-T4JPlz943NyKwkkvn2d5cW31iWhnh1IpAFziLnhiv_e1A8-W2WmZA/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* http://secure-web.cisco.com/1euc3IZmziNkQEGPrbT3j3xXlUcAxPPaKWiZ0CYjU1kQqaDU... http://secure-web.cisco.com/1p0I0MlPLP2kEVo1ksQYIBnuoxvNFaPTiAXjbNDd1Nc09_YzBN4f81rzz2FNNASj6fj_lB4mShJ0iAkGjJlacAQUSIoirOuw9pl2pXkrsC_w_1GtWWaGWGXtBRKU8HpRw6ddhsrxyxdB3roU2OFr1Q-U6UGiUimVKCEbJdZIzmuonuQhGNIu6fcAPdg0T7vll8arN5C1dr7U9InoGTVh-wZKUGZ9E7G-8ripFKLcUiOl7riHXup5e7cFpD_KkcOtMtavaFtkjjAVW048yfAQHPg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Ah, I see. Please add this at the top of your job: setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
Although trac-all takes care of this when you use ANTs morphs, when you submit jobs separately these jobs don't call trac-all. I'll fix this too in the next version, but for now you have to setenv for every job.
Thanks again for catching these things!
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com Sent: Thursday, July 22, 2021 12:11 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Thanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, 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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Wednesday, July 21, 2021 2:54 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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I used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, 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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Tuesday, July 20, 2021 2:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Hi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
* I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them. * During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist). * trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0-beta/https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Sunday, July 18, 2021 2:18 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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You're welcome 😀 But the problem still remains.
I am using ubuntu (bash shell) thus I added "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" to the first line of the "jobs" file but the issue remained. Should I add value after it? Maybe "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this: cat jobs_prep | parallel -j 10 (to allocate 10 cores).
On Thu, Jul 22, 2021 at 9:09 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Ah, I see. Please add this at the top of your job: setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
Although trac-all takes care of this when you use ANTs morphs, when you submit jobs separately these jobs don't call trac-all. I'll fix this too in the next version, but for now you have to setenv for every job.
Thanks again for catching these things!
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Thursday, July 22, 2021 12:11 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionThanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Wednesday, July 21, 2021 2:54 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionI used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Tuesday, July 20, 2021 2:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence,
thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
- During trac-all -prep there were errors of pathlist and trclist; it
was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
- trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jYJlRtsG56HVKexWP536EPiFzT0mvnrG_krTS2DBuokAmI... https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pG0XRSroR8mJ1LvuC8zbhxdX1hqiEm68ALUIaxhjVV5A1a... https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1sobX6uQs1B6SFJhnUYURbnrHgMFWVA2OPXbCy3pOYnv_4p... https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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* http://secure-web.cisco.com/1VCPhXJJj3kFaSfTmXjzu21XvmKrPR2G-Q3SLwCL2mYfHJsY... http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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/1sobX6uQs1B6SFJhnUYURbnrHgMFWVA2OPXbCy3pOYnv_4p... https://secure-web.cisco.com/15pumBR0k2yUDnVLRQXHbamJjtKkhtAOwRY_gZg9xgRGpTfAoFrv0QvlfC8XEntCh_LqVkxnOorujG_MK7xW2tym3k6rT2z_soL8mv12tCTF802YI75-IKLu2zokLgiBM3qOFFXz7oExbR9PUxvfIqwX8AfH5dAQbKSYTuPyfDsUAjNZoUE2aTiK2SvrM--a3c_XRgNVnMGkIq-PukmOVK1GEpxOZrF_e-T4JPlz943NyKwkkvn2d5cW31iWhnh1IpAFziLnhiv_e1A8-W2WmZA/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* http://secure-web.cisco.com/1VCPhXJJj3kFaSfTmXjzu21XvmKrPR2G-Q3SLwCL2mYfHJsY... http://secure-web.cisco.com/1p0I0MlPLP2kEVo1ksQYIBnuoxvNFaPTiAXjbNDd1Nc09_YzBN4f81rzz2FNNASj6fj_lB4mShJ0iAkGjJlacAQUSIoirOuw9pl2pXkrsC_w_1GtWWaGWGXtBRKU8HpRw6ddhsrxyxdB3roU2OFr1Q-U6UGiUimVKCEbJdZIzmuonuQhGNIu6fcAPdg0T7vll8arN5C1dr7U9InoGTVh-wZKUGZ9E7G-8ripFKLcUiOl7riHXup5e7cFpD_KkcOtMtavaFtkjjAVW048yfAQHPg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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External Email - Use Caution
An update:
I tried to change the shell into tcsh (exec /bin/tcsh) temporarily but other errors appeared. I added "setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" at the beginning of the $FREESURFER_HOME/bin/trac-preproc and the problem is now solved.
Cheers! Amir
On Thu, Jul 22, 2021 at 11:52 PM AmirHussein Abdolalizadeh < amirhussein.a@gmail.com> wrote:
You're welcome 😀 But the problem still remains.
I am using ubuntu (bash shell) thus I added "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" to the first line of the "jobs" file but the issue remained. Should I add value after it? Maybe "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this: cat jobs_prep | parallel -j 10 (to allocate 10 cores).
On Thu, Jul 22, 2021 at 9:09 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Ah, I see. Please add this at the top of your job: setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
Although trac-all takes care of this when you use ANTs morphs, when you submit jobs separately these jobs don't call trac-all. I'll fix this too in the next version, but for now you have to setenv for every job.
Thanks again for catching these things!
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Thursday, July 22, 2021 12:11 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionThanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Wednesday, July 21, 2021 2:54 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionI used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Tuesday, July 20, 2021 2:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence,
thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
- During trac-all -prep there were errors of pathlist and trclist; it
was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
- trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1qBLDmHvTEHeqS6J3zmWlC8rV8yM-EEnS9WQRuicbApuonl... https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/190as38pI3YOKXutSDLsB0SvK6KIyCDP5VnebfQqnA0RUrO... https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1_v1DsFrOupq_QuuHJvsFmYh4D4P78giQPV_uNo7cXwJF_U... https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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* http://secure-web.cisco.com/16sV2GpeCBR-Yo8KAaWBbygc9Aquky9Pvbmru2pkk5_NzAhj... http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Glad to hear that worked. Again, just a temporary fix until the next version comes out. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com Sent: Friday, July 23, 2021 5:51 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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An update:
I tried to change the shell into tcsh (exec /bin/tcsh) temporarily but other errors appeared. I added "setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" at the beginning of the $FREESURFER_HOME/bin/trac-preproc and the problem is now solved.
Cheers! Amir
On Thu, Jul 22, 2021 at 11:52 PM AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> wrote: You're welcome 😀 But the problem still remains.
I am using ubuntu (bash shell) thus I added "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" to the first line of the "jobs" file but the issue remained. Should I add value after it? Maybe "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this: cat jobs_prep | parallel -j 10 (to allocate 10 cores).
On Thu, Jul 22, 2021 at 9:09 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ah, I see. Please add this at the top of your job: setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
Although trac-all takes care of this when you use ANTs morphs, when you submit jobs separately these jobs don't call trac-all. I'll fix this too in the next version, but for now you have to setenv for every job.
Thanks again for catching these things!
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Thursday, July 22, 2021 12:11 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Thanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, 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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Wednesday, July 21, 2021 2:54 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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I used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, 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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Tuesday, July 20, 2021 2:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Hi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
* I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them. * During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist). * trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0-beta/https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Sent: Sunday, July 18, 2021 2:18 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
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Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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External Email - Use Caution
Hi Anastasia,
Now that I have completed all the processes (except -stats) I want to share any other issues that I encountered to first, know your opinion, and second, it may become handy for anyone tries to use TRACULA until the fix comes out:
After the issues encountered in the -prep that we solved, I started -bedp with -jobs {jobs}. Using it produces three files for parallel computing: pre.{jobs}, {jobs}, and post.{jobs}. Running them in the mentioned order caused a few issues:
- A few directories are required to be built manually prior to the analysis: ${subj}/dmri.bedpostX, dmri.bedpostX/logs, dmri.bedpostX/logs/monitor, and dmri.bedpostX/xfms - Running bedpostx_preproc.sh caused an error in line 79 of the code: there is an "if" with -eq option which is an "unexpected operator" (FSL v6.0.4). I think what they meant was -e instead of -eq. After changing it I had no problems.
In the end, thanks for this great tool!
Bests, Amir
On Fri, Jul 23, 2021 at 6:30 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Glad to hear that worked. Again, just a temporary fix until the next version comes out.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Friday, July 23, 2021 5:51 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionAn update:
I tried to change the shell into tcsh (exec /bin/tcsh) temporarily but other errors appeared. I added "setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" at the beginning of the $FREESURFER_HOME/bin/trac-preproc and the problem is now solved.
Cheers! Amir
On Thu, Jul 22, 2021 at 11:52 PM AmirHussein Abdolalizadeh < amirhussein.a@gmail.com> wrote:
You're welcome 😀 But the problem still remains.
I am using ubuntu (bash shell) thus I added "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" to the first line of the "jobs" file but the issue remained. Should I add value after it? Maybe "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this: cat jobs_prep | parallel -j 10 (to allocate 10 cores).
On Thu, Jul 22, 2021 at 9:09 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Ah, I see. Please add this at the top of your job: setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
Although trac-all takes care of this when you use ANTs morphs, when you submit jobs separately these jobs don't call trac-all. I'll fix this too in the next version, but for now you have to setenv for every job.
Thanks again for catching these things!
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Thursday, July 22, 2021 12:11 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionThanks! I also encountered an error while running -prep using parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I couldn't find any relevant information searching the forum nor I couldn't solve it after a few tries. I didn't encountered this error while running it on my pilot subject (the protocols are same):
In the subjects: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
However, for the pilot subject it was: mri_vol2vol --gcam /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0 0 /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz Loading mov /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz Loading source LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta Loading GCAM /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Inverting Source LTA WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox MRIvol2volGCAM: t=0.4239 Writing to /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz mri_vol2vol gcam done [and continues without error]
The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion.
Bests, Amir
On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.
The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.
I'll fix the example file and make the documentation clearer on this point.
Thanks for bringing this to our attention, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Wednesday, July 21, 2021 2:54 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionI used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.
Bests, Amir
On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported 🙂
About the second issue, was there something in your config file about where to find the training data, or did you just use the default?
Thanks, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Tuesday, July 20, 2021 2:17 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia,
I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:
- I did thalamic segmentation using the T2 beside the T1 sequence,
thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
- During trac-all -prep there were errors of pathlist and trclist; it
was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
- trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.
I hope they've been addressed in the released 7.2 version.
Bests, Amir
On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Amir - You can check the build stamp in your log file:
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1BAqsmBo-iErXGocIs8JD8eQRmQb6Jpji5plIa0pLCRVfBq... https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.
I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1HCol9wPj-dlWwoHkOQYCy6CBmgMqdFTiKAVcKkNAlZWqWG... https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
Let us know how it goes! 🙂
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Sent:* Sunday, July 18, 2021 2:18 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
External Email - Use CautionHi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using? _______________________________________________ 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/1pSUUFtiMOo6i31v3N4l9r4j8EbbbAm9Vrf-0jmpQYDs24t... https://secure-web.cisco.com/1kAvp44ZxJ5MTHJdbjAMlxH1yGojhSEW1e1oDlFBn8IQHT8y_c8V0EBTlOmpIpmP6SIWPugmNff-gDvTRDJU-TMLUGTOLQctf6Lk403exnrauHXFXLKALjDiJxQYJtkF1ZFaKjGncs-_qX7k6k5Njss2Q7TqfV6hxPHI_zk7FiMONRfCzTBur10VSZRk9xvxmgsJKlkxbXfkW0WJd0RNeNrCH8PrXtXwhUiLj5vtu21d87DCYz3MJNy2I3zA6CDypmvA74kskprOAzwCofjLnQQ/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* http://secure-web.cisco.com/1MLV6iTS6S2igDaqAD1IPw5rwWe8RTb5Z4Giv6zlbU_rwFXJ... http://secure-web.cisco.com/166ZfxaPD2Muh2NJXl5MBRPZHdSrQjfsjyIeanoGLOJaj0GmbX8_1kGJfCrJmXv4vwtZpjk86gOWsS59t6XygluXNAm9Cvite5hacd48HT4FBfus_5cdLXaX9z4jJ-cdfthtA3aS9qlND6oLkmkRB9sZq5Q-9u7wMVxvp3ZBq9blnWF4PcM6R4gjHKLjZZYHBSDLiJwMc0qfCPAOdN7LB0-dKL46jC6LxgHgtBYXtsDPtV_zHlsQmuzKjajP3KIC_JQl6E5t8bdHiLSj3PPrddg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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freesurfer@nmr.mgh.harvard.edu
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AmirHussein Abdolalizadeh -
Yendiki, Anastasia