Replace fsl split #548
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Replace fsl split #548
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Thank you!! Did you get a chance to try this on local data to see if the quartering artifact pops up? One of the places I suspected might have introduced this is if TSplit changes the header in the split images |
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I was also wondering if this was the culprit actually. It ran fine with a similar build on some ABCD data. I also left in FSL's Split function for FSL workflows, and it was a TOPUP test failing that alerted me to the initial problem. So I think with all the circleCI tests passing we have solid evidence that this isn't the issue. |
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Changes proposed in this pull request
Part of a series of branches and PRs addressing issue #482.
Replaces FSL's Split function with AFNI's 3dTsplit (for the DWI files) and custom code (for bvals and bvecs). Outputs and inputs should match the previous version exactly. FSL Split is still used in workflows that otherwise require FSL (e.g. eddy).
Documentation that should be reviewed