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
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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-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
20190730_601840595_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE_bvals
Description: 20190730_601840595_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE_bvals
20190730_601840595_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE_bvecs
Description: 20190730_601840595_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE_bvecs
0 -0.793264 -0.453844 -0.279937 0.976579 0.920768 -0.109425 0.797352 0.40927 0.7185 0.148134 0.874533 -0.71854 0.25906 -0.168541 0.316621 -0.0636804 -0.537506 0.75459 -0.706812 0.841903 0.965219 0.473258 0.777221 -0.306158 0.352246 0.0510634 -0.295841 -0.148146 0.292773 -0.582397 -0.49092 0.0527806 0.6408 -0.940995 -0.378689 0.556942 -0.841237 0.390197 -0.540939 -0.515225 0.0665532 0.003517 -0.870682 0.646039 -0.337509 -0.977518 -0.185139 -0.111416 0.530687 0.515277 0.144233 0.114025 -0.690983 0.456444 -0.953231 -0.452436 -0.760216 0.732866 0.219071 -0.787297 0.999853 -0.00506 0.01641 0.703424 0.718606 0 -0.394167 0.224623 -0.0490364 -0.104937 -0.249138 -0.741243 0.0270038 0.819499 0.695525 0.133883 0.376044 -0.695483 -0.957407 0.978485 0.947904 0.941294 -0.718571 0.503301 0.453903 -0.534426 0.215635 -0.191955 0.0719707 -0.95198 -0.665125 -0.953306 0.756432 -0.133975 -0.753247 0.782784 -0.77433 -0.377297 -0.385367 0.0980678 0.639755 0.691604 -0.371009 0.008413 -0.31355 0.822719 0.700213 0.307862 0.490451 -0.705444 0.385112 0.0979165 -0.611278 -0.908207 0.349305 -0.822669 0.874134 0.570052 0.0105631 0.443091 -0.297062 -0.439255 0.477781 -0.438402 -0.40556 0.048099 -0.00835002 -0.978291 0.207071 -0.697661 0.140517 0 0.464074 -0.862305 0.958765 0.187836 -0.300195 0.662257 0.60291 -0.401148 0.00191186 0.979863 0.30624 -0.00198547 -0.127514 0.119002 0.0350666 -0.331526 -0.441297 -0.421049 0.542576 0.0747514 -0.147832 0.859756 -0.625099 0.0013264 0.658431 0.297657 0.583343 -0.979849 -0.588984 0.219233 0.399263 0.924587 -0.663979 0.323901 -0.668811 0.45989 -0.393283 -0.920693 -0.78043 -0.24016 -0.710825 -0.951424 0.0370301 -0.291518 0.858939 -0.186735 -0.769456 -0.40342 0.772242 0.24022 0.463773 0.813658 0.722794 -0.771576 0.0557288 0.776117 -0.440224 0.520299 -0.887428 -0.614695 -0.015006 0.207176 0.978188 0.135885 0.681073
0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0.001 0.001 0.001 0.001 0.001
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