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Hi everyone! I'm almost done with my contribution on the structural connectivity (dMRI) tutorial. However i have a question: Context: During my analysis, i copied the fs_default.txt file and freesurferColorLUT.txt file manually to my subject folders from the mrtrix3 software and $FREESURFERHOME outside neurodesk. Question: |
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Replies: 2 comments 7 replies
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Dear @Joanone, That's fantastic to hear :) Looking forward to see the tutorial! I am not sure I understood the question 100%, but what I understood is: Are fs_default.txt and freesurferColorLUT.txt inside Neurodesk somewhere so you can use them in the mrtrix container? If that was the question, then: Yes, they are in the freesurfer container and the mrtrix container :) You can copy these files from there to a central directory like /neurodesktop-storage/ Cheers |
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I have been trying to submit the tutorial and open a pull request so that it can be reviewed but i'm currently stuck at step 5 in the workflow template stated here: https://www.neurodesk.org/tutorials/documentation/workflowtemplate/ Checking that the pages point to gh-pages, got an error stating that: Domain is not a valid public domain. Domain is not properly formatted. Thanks |
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Dear @Joanone,
That's fantastic to hear :) Looking forward to see the tutorial!
I am not sure I understood the question 100%, but what I understood is: Are fs_default.txt and freesurferColorLUT.txt inside Neurodesk somewhere so you can use them in the mrtrix container?
If that was the question, then: Yes, they are in the freesurfer container and the mrtrix container :)
fs_default.txt is in the mrtrix3 container under: /opt/mrtrix3-3.0.3/share/mrtrix3/labelconvert/fs_default.txt
FreeSurferColorLUT.txt is in the freesurfer container under: /opt/freesurfer-7.2.0/FreeSurferColorLUT.txt
You can copy these files from there to a central directory like /neurodesktop-storage/
Cheers
Steffen