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  • Fidel Alfaro Almagro
  • UKB_UNCONFOUND_v2
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  • !6

Add absolute path to FSL commands

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Open Tom Nichols requested to merge nichols/ukb_unconfound_v2:UseAbsoluteFSLpaths into master Feb 25, 2021
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Inspired by problems in generate_initial_data/gen_STRUCTMOTION/script_STRUCTMOTION_subject.sh, where multiple active versions of FSL lead to an old version of smoothest creating problems, I've gone through and looked for all instances where FSL commands were called and added $FSLDIR/bin/ to make the paths absolute.

The notable exception to this is (1) fsl_sub... it's own evil beast, I didn't want to touch that, and (2) places in Matlab code that I saw call FSL tools with absolute paths... just not sure enough to fix thoses.

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Source branch: UseAbsoluteFSLpaths