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.com> wrote:
You're welcome ðŸ˜€
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
 

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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
 

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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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