External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@einsteinmed.org>
Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Yendiki,
Anastasia <ayend...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list
{Disarmed}
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@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}
CAUTION: This email comes from an external source; the attachments and/or links
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External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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:
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Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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.jayak...@einsteinmed.org>
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia <ayend...@mgh.harvard.edu>
Subject: Fw: Tracula error: run list is longer than subject list
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@einsteinmed.org>
Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Yendiki,
Anastasia <ayend...@mgh.harvard.edu>
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@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
CAUTION: This email comes from an external source; the attachments and/or links
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody
<shanika.jayak...@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
External Email - Use Caution
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
iterations
Description: iterations
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