Timothy B. Brown

I'm not convinced that the proposed change will actually work as expected. The `ContrastNames` variable is populated by a statement that looks like: ContrastNames=`cat ${FirstFolder}/design.con | grep "ContrastName" | cut...

* The goal was for every single command line option is optional. None of them actually have to be specified. If none are specified, then this script is backward compatible...

I've push changes to: * Add a `DEFAULT_RUN_LOCAL` variable * Add a `DEFAULT_LIFESPAN_STYLE` variable * Add comments to more clearly note where changes would be made by a user wishing...

My first cut at this was indeed to create a separate `PreFreeSurferPipelineBatch.sh` that was specific for LifeSpan data. I was either going to keep it in the same directory and...

I've reverted the `PreFreeSurferPipelineBatch.sh` file back to exactly how it was before I started this and created an `Examples/Scripts/LifeSpan/PreFreeSurferPipelineBatch.LifeSpan.sh` file. The `PreFreeSurferPipelineBatch.LifeSpan.sh` file is simplified some since only one version...

The change to just supporting the lowercase version (and only one version) of the command line options has been made in the `PreFreeSurferPipelineBatch.LifeSpan.sh` version of the file.

I conditionally added the `--fmapmag=`, `--fmapphase=`, and `--fmapgeneralelectric=` options to the build of the `PreFreeSurferCmd` in `PreFreeSurferPipelineBatch.LifeSpan.sh`. I expect that there is more work to do to make the building...

I expect that if I had started this set of changes along the lines of copying the original example to create a version for LifeSpan, then it would have ended...