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.