Hi Oshadi - That does not sound normal. Is there anything wrong with the FreeSurfer segmentation of this subject?

Anastasia.

From: Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Monday, November 2, 2020 10:33 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

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Hi Anastasia

Thanks so much- I think I got the error due to the format of the bvecs and bvals

Trac-all is running but for one person it is running for almost 5 days now- I assume that can't be normal?

It says 8/18 tracts are completed but these iterations I have attached in the text files are running for 5 days

I wonder if I should let it run or kill the process

thanks,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Wednesday, October 28, 2020 12:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns are:

0 -0.793264

0 -0.394167

0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:

0 -0.793264 -0.453844

-0.279937 0.976579 0.920768

Which one is the correct version?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

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Also, I am not sure if these are helpful for you to give me a suggestion-but I have attached here our original bvals and bvecs text files and the text files I have formatted according to configuration file tutorial.

I have tried with them both but get the same error

Thank you very much,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

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Hi Anastasia

Thanks so much- it worked! just now.

But I have this error with trac-preprocessing I get "Error: data and bvals/bvecs do not contain the same number of entries"

As far as I know all my files have 66 entries so I am not sure what causes this.

If you have any suggestion please let me know

Thanks,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from "nam04.safelinks.protection.outlook.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

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I am double checking so the command is trac-all -prep -c /path/to/configuration file- is that what you meant?

Thanks,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, not the nifti file.

From: Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Subject: Fw: Tracula error: run list is longer than subject list

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Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the extension (renamed the file too as IM_007.dcm)

Just to see if there is a different outcome, I ran trac-all on another subject too but still I get the same error.

I have two things to double check with you

1) our pre-processed files are nii, not dcm-I have changed the configuration file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did trac-all- this way the first error I get is illigal variable name. I am not sure if nii files won't work or if there is something wrong with my configuration file.

2) I ran trac-all on the same subjects dicom files (changed the configuration file accordingly)

Either way I get the same error (log file attached). It would be really great if you can suggest something-looking forward to hear from you.

Many thanks,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,

Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list

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Hi Anastasia

Thanks again for helping with troubleshooting the error- I was wondering if you have any suggestions for me to try.

I have also tried running TRACULA on freesurfer tutorial data but get the same error

Best regards,

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

External Email - Use Caution

Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)

I have attached the

1) log file

2) cognfiuration file

3) bvec and bval files I have used.

I hope that's what you need- I am very new to FreeSurfer please let me know if you want me to send any more files.

Thank you for your help

Best regards

Oshadi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then please attach your log file and configuration file - it's hard to guess the issue without more information.

Best,
Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody@einsteinmed.org>
Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Tracula error: run list is longer than subject list

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Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list"

I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about.

I wonder if anyone can help me figure out a solution.

Many thanks

Oshadi