Comments (6)
Chris and I had discussed this when I added the resume_cmd
for Issue #7, the reason for the current checks is to allow for resuming stages after manual correction, but still allowing for the novice, "run it again to rewrite everything" behavior.
This would change the default behavior to skipping subjects if the subject directory exists unless force-recompute is present, but if you want to run e.g., autorecon3, you would also have to set force-recompute, which may be confusing, but could be explained.
Chris, what do you think?
An alternative could be a --longitudinal2
switch which goes straight to base and long (maybe using the dontrun
stages flag).
On further reviewing the code, I believe the stages
options is missing from the first round run.py lines 158 and 162
, which also needs to be fixed.
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On further reviewing the code, I believe the stagesoptions is missing from the first round run.py lines 158 and 162, which also needs to be fixed.
That's probably on purpose. If only parts of recon-all -all
is run at the cross-sectional phase, it think it is not possible to create a base image.
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Ahoi hoi @fliem and @alexlicohen,
was there any further discussion re this?
Otherwise, we could close this issue.
Cheers, Peer
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Ok, thx @alexlicohen!
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