Convert longitudinal FS to new I/O interface library

[glasserm]

Hi Jure,

Would you be willing to convert this code to the new I/O interface library that Tim Coalson wrote? It is much simpler to use than the style this is currently in (which comes from Tim Brown)?

https://github.com/Washington-University/HCPpipelines/blob/94d31f411d2552b775776a24ad14bedfbec9b9ce/FreeSurfer/LongitudinalFreeSurferPipeline.sh

Thanks,

Matt.

[demsarjure]

Yeah, sure. Can you just point me to a recent use of the new interface, so I do not use something outdated again. Thanks!

[glasserm]

The new PreFreeSurfer is an example. If you like, you could wait till Yash converts FreeSurfer for a very similar example.

[demsarjure]

I will wait for FreeSurfer since it is much more similar and will be easier to use for adaptation.

[coalsont]

You can also look at the simple example at the top of newopts.shlib:

https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/newopts.shlib

This section is meant to be copypasted into a new file as a starting point for any new script in the pipelines. Fill out the arguments section, and write the processing code below the whole thing.