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pnlbwh / luigi-pnlpipe

NIFTI pipeline glued together using Luigi
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index.txt instructions #70

Open RyanZurrin opened 1 month ago

RyanZurrin commented 1 month ago

Add documentation on how to create a proper index.txt file for synb0 or other tasks.

tashrifbillah commented 1 month ago

We had referred users to FSL documentation in the past who are the creators of index.txt:

http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/tutorial_packages/centos6/fsl_507/doc/wiki/eddy(2f)UsersGuide.html#A--index

RyanZurrin commented 1 month ago

yes but this requires the users to first try running things and then to come to us to ask, I am thinking if you just include a paragraph that says:

"To set up the index.txt, use fslhd or fslinfo to check dim4 value of your data. The Value of dim4 will determine how many 1's seperated by spaces there are. For example say there is dim4=6, then the index.txt will be: ```1 1 1 1 1 1```` "