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
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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-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