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 <
ayend...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
> Abdolalizadeh <amirhussei...@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 <
> ayend...@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_RLLijNVHwoesce4ZNdwZezMULRt2tNtPfszwi2gtQPwyVit6D529yV0YbVO3uAvDkYS6sh-7ujP2pUDOrCg53TqwaJjcyXusmutgLi8lGL3b9Hzsw-z4BwSNRbyuy9Uuo9uMmuUkzxAVHh_bwmUmDOTSCzQFPYyaNRkUuIiZOcrENAcqiwt_KIT6jB1RBtMiGV0BuFqAviiiJvVjBpt_CdiWmnoYpLsGKGPIJt1L-lA9knvvXV0Fb2MpWI0rA_Mg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
> <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_2qtOlHo7gVC1Bsl0hIvNfuS_4ScLrnLO9Y-vcDd8Ad4UB0VX9C4WHduzTCXUtsp1qpu3zUhUajYaVfYB2tJBJdUujuALwFb5TNtanP5W5EwKEOXYEJQLkoz5uJg8dNNUr2NP0DkE5llnZN-qwJgJ1kPLq7g6GJxfLfYck8DN7b9fOSDljhb320JWWxPH2ErcGvCACUNg8sZhI6HlAiVn_CvKas3X4qvJ4syahtyf-AT1Exmc2rVoK7OlNrviLA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
> <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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
> Abdolalizadeh <amirhussei...@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?
> _______________________________________________
> 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_gZg9xgRGpTfAoFrv0QvlfC8XEntCh_LqVkxnOorujG_MK7xW2tym3k6rT2z_soL8mv12tCTF802YI75-IKLu2zokLgiBM3qOFFXz7oExbR9PUxvfIqwX8AfH5dAQbKSYTuPyfDsUAjNZoUE2aTiK2SvrM--a3c_XRgNVnMGkIq-PukmOVK1GEpxOZrF_e-T4JPlz943NyKwkkvn2d5cW31iWhnh1IpAFziLnhiv_e1A8-W2WmZA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> <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_YzBN4f81rzz2FNNASj6fj_lB4mShJ0iAkGjJlacAQUSIoirOuw9pl2pXkrsC_w_1GtWWaGWGXtBRKU8HpRw6ddhsrxyxdB3roU2OFr1Q-U6UGiUimVKCEbJdZIzmuonuQhGNIu6fcAPdg0T7vll8arN5C1dr7U9InoGTVh-wZKUGZ9E7G-8ripFKLcUiOl7riHXup5e7cFpD_KkcOtMtavaFtkjjAVW048yfAQHPg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <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_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
> 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.
>
dmrirc.722.pilot
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
