What goes after "-c" in the trac-all command should be the configuration file,
not the nifti file.
________________________________
From: Shanika Jayakody <[email protected]>
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia <[email protected]>
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: [email protected]
<[email protected]> on behalf of Yendiki, Anastasia
<[email protected]>
Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list <[email protected]>
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: [email protected]
<[email protected]> on behalf of Shanika Jayakody
<[email protected]>
Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list <[email protected]>; Yendiki,
Anastasia <[email protected]>
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: [email protected]
<[email protected]> on behalf of Shanika Jayakody
<[email protected]>
Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list <[email protected]>
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
may compromise our secure environment. Do not open or click on suspicious
emails. Please click on the “Phish Alert” button on the top right of the
Outlook dashboard to report any suspicious emails.
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: [email protected]
<[email protected]> on behalf of Yendiki, Anastasia
<[email protected]>
Sent: Monday, October 19, 2020 8:33 PM
To: [email protected] <[email protected]>
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: [email protected]
<[email protected]> on behalf of Shanika Jayakody
<[email protected]>
Sent: Monday, October 19, 2020 2:43 PM
To: [email protected] <[email protected]>
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
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
