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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.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.