Brainstorm/implement command-line parameters

gdevenyi commented 8 years ago

Need to start making script flexible brainstorming list

[x] run up until specific stage
[x] run specific stage only (with warning)
[x] override atlas/template/subject detected resolution
[x] forcing highmem
[x] specify registration command
[ ] specify resample command
[ ] specify voting command
[ ] turn on/off morpho
[x] dryrun mode
[x] proper status mode (count all the possibilities for outputs)
[x] run for specific subject
[ ] run basic preprocessing

Probably implement with getopts http://tuxtweaks.com/2014/05/bash-getopts/

Stages should be changed to functions to allow for cleaner looking stage-control logic

gdevenyi commented 8 years ago

Waiting on https://github.com/kvz/bash3boilerplate/issues/23 for some of these

egarza commented 8 years ago

With my .45 x .45 x 1 mm data I already had a walltime problem. So, modifying walltime would be a nice feature out-of-the-box.

gdevenyi commented 8 years ago

As per comment above, modification is waiting on long-form option parsing. In the meantime, you can edit the walltimes manually in stages.sh. See https://github.com/CobraLab/antsRegistration-MAGeT/issues/20 for benchmarking of walltime/memory for single antsRegistration runs.

CoBrALab / antsRegistration-MAGeT

Brainstorm/implement command-line parameters #32