Example: Resting preprocessing workflow #646
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updated changes!
…nh/restingwf Conflicts: examples/rsfmri_preprocessing.py
Enh/restingwf
* fix/mapnode: fix: added forced removal and running of multiple hashfiles fix: remove json files when rerunning a mapnode Add test for SelectFiles force_lists error Check that force_lists fields have templates Enhance flexibiliy of SelectFiles output list coercion without this, line 151 tries to call a module
…e from mindboggle
…h/restingwf Conflicts: examples/rsfmri_preprocessing.py
* master: tst: added test for extra json tst: added test for mapnode multiple json failure fix: remove only json hash files Fixed filenames in documentation Added dummy files so doctest doesn't fail PEP8 for the whole interface Run autopep8 on misc.py Added inputs&outputs descriptions Working version Base class for FuzzyOverlap misc tool
* master: doc: minimal provenance documentation Minor detail fixed Fix for FUGUE interface
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| python rsfmri_preprocessing.py -d /data/12345-34-1.dcm -f /data/Resting.nii -s subj001 -n 2 --despike -o output -p "plugin_args=dict(plugin='PBS', plugin_args=dict(qsub_args='-q many'))" |
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It definitely seems like the -p argument here can be shortened and then handled internally. Why not just -p PBS and -q many? Having people write Python strings on the command line is just asking for annoying errors.
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the intent was to allow any nipype plugin to be used from the command line. i haven't figured out a good way to encapsulate those semantics.
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But plugin just takes a string anyway. I agree the plugin_args are little harder to extract, but even just exposing a few general things (-queue, -nprocs) and leaving the option of of specifying the rest with a string seems better.
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Looks like the |
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that's a regular python function. i can take those out. but they won't come through imports. |
…e copied or not. in case inputs are directories, this will allow refreshing outputs.
* master: removed save_warped flag from FUGUE call since it doesn't seem to exist in the FUGUE interface try to determine output dir from fsf file, to deal with cases where the output dir is not in the cwd
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I think i would continue to advocate for doing |
Example: Resting preprocessing workflow
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