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-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

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: 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

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

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-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

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-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

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: 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

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