from nipype import SelectFiles, Node
# String template with {}-based strings
templates = {'anat': 'sub-01/ses-*/anat/sub-01_ses-*_T1w.nii.gz'}
# Create SelectFiles node
sf = Node(SelectFiles(templates),
name='selectfiles')
# Location of the dataset folder
sf.inputs.base_directory = '/data/ds000114'
#sf.inputs.ses_name =
sf.run().outputs
from nipype import MapNode
template = {'anat': 'sub-{subject_id:02d}/ses-{ses_name}/anat/*_T1w.nii.gz'}
sf = MapNode(SelectFiles(template,
force_lists=True,
base_directory='/data/ds000114/'),
iterfield=['subject_id', 'ses_name'],
name='select_files')
sf.inputs.subject_id = [1, 1]
sf.inputs.ses_name = ['test', 'retest']
sf_res = sf.run()
sf_res.outputs
This seems like kind of a crappy solution though, because if you want to get more than one subject you're typing out:
sf.inputs.subject_id = [1, 1, 2, 2]
sf.inputs.ses_name = ['test', 'retest', 'test', 'retest']
# write your solution here
from nipype import JoinNode, Node, Workflow, Function
template = {'anat': 'sub-{subject_id:02d}/ses-{ses_name}/anat/*_T1w.nii.gz'}
sf = Node(SelectFiles(template,
force_lists=True,
base_directory='/data/ds000114/'),
name='select_files')
sf.iterables = [('subject_id', (1,2)),
('ses_name', ('test', 'retest'))]
combine = lambda anat:list(anat)
jn = JoinNode(Function(input_names=['anat'],
output_names=['anat'],
function=combine),
name='join_anat',
joinsource=sf,
joinfield='anat'
)
def unpack_list(x):
out_list = []
for xx in x:
out_list.extend(xx)
return out_list
un = Node(Function(input_names=['x'],
output_names=['anat'],
function=unpack_list),
name='unpack_anat')
wfsf = Workflow('sf_iterable', base_dir='/output/working_dir/')
wfsf.connect([(sf, jn, [('anat', 'anat')]),
(jn, un, [('anat', 'x')])])
sf_res = wfsf.run()
print([nn.result.outputs for nn in list(sf_res.nodes) if nn.name == 'unpack_anat'])
So my question is, what's going on here? I feel like I must be misunderstanding how to use SelectFiles.
Also, the tutorial should maybe point out the potential bug in which you specify base_dir inside the SelectFiles definition instead of base_directory.
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