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
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.
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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
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-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
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.
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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
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
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:
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
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-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
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
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-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:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTraculahttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C2c61f34fe1ea4e1aab4d08d87aa7c4e2%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394208616072027%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=NCzjceGf1ddPm6iE0h9zOL2kfuJal6LwI0IxrMeOAbc%3D&reserved=0
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
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-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
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
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-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}
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 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/RunningTraculahttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C365d1f7e99384045bef308d87aa85f54%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394211236261729%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=t48AibkW%2FzZPCiHBgie9eGu4ag7rM8P%2Fh2WCT1mwzW0%3D&reserved=0
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
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.
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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
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}
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.
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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/RunningTraculahttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula&data=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C365d1f7e99384045bef308d87aa85f54%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637394211236261729%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=t48AibkW%2FzZPCiHBgie9eGu4ag7rM8P%2Fh2WCT1mwzW0%3D&reserved=0
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
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
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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
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.
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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
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 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}
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-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}
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.
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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://secure-web.cisco.com/1J5hh7AgcOj1tdo-va-kiSPXCzMxQmIMchhFPavlfopBQeN...https://secure-web.cisco.com/146GojQy4RiAvlA_6zW8bT2ny-knf7zanWC8SrvCeKZ-CR_2OUpWP5UDeNRcx3aIZH6-15JLfEJpvg9t75ZtsTYRMyjiAFzwmL0KJcumHCDsjsshLweBsuT8c7_HQvs_iz-brFCBH1XxZHnJIykqFyIstp69xv3rrCnSOedkMWD1bd42wRk3m-pc9W5iEAl90qSK_rdcNFuofSWbPeFfDFA/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FRunningTracula%26data%3D04%257C01%257Cshanika.jayakody%2540einsteinmed.org%257C0753eb6c20fa48735e9908d87af7b98a%257C9c01f0fd65e040c089a82dfd51e62025%257C0%257C0%257C637394551681983427%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D6VAL6DtX%252F%252FxJ2BaHKhLZaW438KJ3mqIrz69Iwb%252FkNJA%253D%26reserved%3D0
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
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
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}
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-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:
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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
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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
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Hi Anastasia- Thank you for your reply! I will try another subject and see.
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, November 2, 2020 11:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}
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}
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-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}
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.
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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:
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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
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.
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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
freesurfer@nmr.mgh.harvard.edu
-
Shanika Jayakody -
Yendiki, Anastasia