Chris Gorgolewski chrisgorgo
chrisgorgo
/ gist:359040
Created
April 7, 2010 15:50
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| Case 1 | |
| SubjectSource ->['4D.nii']->Spm.Realign->'4D.nii'->FSL.Smooth->'4D.nii' | |
| in contrast to: | |
| SubjectSource ->['4D.nii']->Spm.Realign->['4D.nii']->FSL.Smooth->'4D.nii' | |
| Case 2 | |
| SubjectSource ->['4D.nii']->Spm.Realign->'4D.nii'->SPM.Smooth->'4D.nii'->FSL.Bet | |
| even thou SPM.Smooth also accept lists |
chrisgorgo
/ gist:359398
Created
April 7, 2010 20:22
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| ''' | |
| Created on Apr 7, 2010 | |
| @author: filo | |
| ''' | |
| from nipype.interfaces.base import traits, isdefined | |
| from enthought.traits.has_traits import HasTraits | |
| class OutputMultiPath(traits.List): | |
| """ Implements a user friendly traits that accepts one or more |
chrisgorgo
/ gist:360464
Created
April 8, 2010 20:01
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| ''' | |
| Created on Apr 7, 2010 | |
| @author: filo | |
| ''' | |
| from nipype.interfaces.base import traits, isdefined, TraitedSpec | |
| from enthought.traits.trait_base import _Undefined | |
| class OutputMultiPath(traits.List): | |
chrisgorgo
/ gist:361167
Created
April 9, 2010 13:39
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| ''' | |
| Created on Apr 7, 2010 | |
| @author: filo | |
| ''' | |
| from nipype.interfaces.base import traits, isdefined, TraitedSpec | |
| from enthought.traits.trait_base import _Undefined | |
| class MultiPath(traits.List): | |
| info_text = 'a list of paths' |
chrisgorgo
/ gist:368514
Created
April 16, 2010 14:57
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| filo@filo-dtc:~/workspace/nipype-git/examples$ python spm_tutorial2.py | |
| 4.1.5 | |
| /usr/lib/pymodules/python2.6/foolscap/banana.py:2: DeprecationWarning: the sets module is deprecated | |
| import struct, sets, time | |
| INFO:workflow:in: ('func', 'preproc.realign.infile') | |
| INFO:workflow:in: ('struct', 'preproc.coregister.target') | |
| INFO:workflow:in: ('struct', 'preproc.normalize.source') | |
| INFO:workflow:in: ('subject_id', 'analysis.modelspec.subject_id') | |
| INFO:workflow:in: (('subject_id', <function subjectinfo at 0x334e050>), 'analysis.modelspec.subject_info') | |
| INFO:workflow:out: ('analysis.contrastestimate.con_images', 'contrasts.@con') |
chrisgorgo
/ gist:368520
Created
April 16, 2010 15:02
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| filo@filo-dtc:~/workspace/nipype-git/examples$ ipython spm_tutorial2.py | |
| 4.1.5 | |
| /usr/lib/pymodules/python2.6/foolscap/banana.py:2: DeprecationWarning: the sets module is deprecated | |
| import struct, sets, time | |
| INFO:workflow:in: ('func', 'preproc.realign.infile') | |
| INFO:workflow:in: ('struct', 'preproc.coregister.target') | |
| INFO:workflow:in: ('struct', 'preproc.normalize.source') | |
| INFO:workflow:in: ('subject_id', 'analysis.modelspec.subject_id') | |
| INFO:workflow:in: (('subject_id', <function subjectinfo at 0x1f320c8>), 'analysis.modelspec.subject_info') | |
| INFO:workflow:out: ('analysis.contrastestimate.con_images', 'contrasts.@con') |
chrisgorgo
/ gist:456117
Created
June 28, 2010 17:19
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| from enthought.traits.has_traits import HasTraits | |
| from enthought.traits.trait_base import Undefined | |
| from copy import deepcopy | |
| from nipype.interfaces.traits import File | |
| a = HasTraits() | |
| a.add_trait('foo', File(exists=True)) | |
| a.foo = Undefined |
chrisgorgo
/ ipython_bug.py
Created
July 14, 2010 13:16
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| from IPython.kernel import client | |
| from nodes import DummyClass #change to wherever you've put DummyClass | |
| taskclient = client.TaskClient() | |
| cmdstr = "result = task.run()" | |
| task = client.StringTask(cmdstr, | |
| push = dict(task=DummyClass()), | |
| pull = 'result') |
chrisgorgo
/ gist:573621
Created
September 10, 2010 13:32
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| filo@filo-dtc:~/workspace/nipype$ git checkout 8c388d3262b1b3eedf79 | |
| Note: checking out '8c388d3262b1b3eedf79'. | |
| You are in 'detached HEAD' state. You can look around, make experimental | |
| changes and commit them, and you can discard any commits you make in this | |
| state without impacting any branches by performing another checkout. | |
| If you want to create a new branch to retain commits you create, you may | |
| do so (now or later) by using -b with the checkout command again. Example: |
chrisgorgo
/ gist:578265
Created
September 13, 2010 23:40
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| DEBUG:workflow:Collecting precomputed outputs: | |
| DEBUG:workflow:Aggregate: False | |
| DEBUG:workflow:setting input: level1.smooth0->level1.analysis.modelspec30 {'connect': [('smoothed_files', 'functional_runs')]} | |
| DEBUG:workflow:setting node input: functional_runs->['/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf3.nii', '/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf5.nii', '/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf7.nii', '/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf10.nii'] | |
| DEBUG:workflow:setting nodelevel input functional_runs = ['/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf3.nii', '/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf5.nii', '/media/sdb2/nipype_examples/bootstrapping/workingdir/level1/_subject_id_s1/smooth/srf7.nii', '/media/sdb2/nipype_examples/bootstrapping/worki |
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