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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.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
 

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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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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: 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/

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
 

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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?
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