Hi Doug, 

probably something went wrong during the editing. E.g maybe you edited
files in the cross sectional or base directories and copied/saved these
to the longitudinals or vice-verca. There should be no mis-alignments. 

I would recommend this:

1. run one such subjects without edits through cross, base and long

2. if that looks good, run cross do finalsurf edits if necessary and
complete cross runs. Then run base, do finalsurf edits and complete
base run. Finally run long. All should be fine.

Depending on the type of problem you are editing, usually it is
sufficient to edit these only in the base. 

And make sure you use fs60 (not sure which version you used). 

Best, Martin

On Fri, 2019-09-13 at 16:41 +0000, Douglas Merkitch wrote:
>         External Email - Use Caution        
> Hey all,
> I have a group of subjects with 2 time points that I've run thru the
> longitudinal processing stream. All goes OK until I run the recon-all 
> -long and the resulting .long. subject dirs have the finalsurfs
> misaligned (i.e. one subject has the edits moved inferior and the
> other has them moved superior, causing drastic consequences to the
> pial/wm surfaces).
> FYI these subjects were processed on a Linux-based high performance
> computing cluster and edits were made locally on a Linux virtual
> machine with subject dirs being transferred back and forth via scp.
> Not sure if this is relevant, but thought I’d mention it just in
> case.
> I’ve uploaded a .tar file containing one of these longitudinal
> subject’s directories (i.e. both cross tps, base, and both resulting
> long tps) called ‘merkitch_upload_201980913.tar’ via the filedrop
> website.
> Any help would be appreciated!
> Thanks,
> Doug
> Douglas Merkitch
> Clinical Research Coordinator
> 355 E. Erie St, Chicago, IL 60611
> 312-238-5911 office
> dmerki...@sralab.org
> sralab.org
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