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DOCTEST: Drop doctest SKIP directives
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nibabel/cifti2/cifti2_axes.py

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@@ -67,20 +67,20 @@
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These can be concatenated in a single brain model covering the left cortex and thalamus by
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simply adding them together
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>>> bm_full = bm_cortex + bm_thal # doctest: +SKIP
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>>> bm_full = bm_cortex + bm_thal
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Brain models covering the full HCP grayordinate space can be constructed by adding all the
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volumetric and surface brain models together like this (or by reading one from an already
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existing HCP file).
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Getting a specific brain region from the full brain model is as simple as:
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>>> assert bm_full[bm_full.name == 'CIFTI_STRUCTURE_CORTEX_LEFT'] == bm_cortex # doctest: +SKIP
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>>> assert bm_full[bm_full.name == 'CIFTI_STRUCTURE_THALAMUS_LEFT'] == bm_thal # doctest: +SKIP
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>>> assert bm_full[bm_full.name == 'CIFTI_STRUCTURE_CORTEX_LEFT'] == bm_cortex
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>>> assert bm_full[bm_full.name == 'CIFTI_STRUCTURE_THALAMUS_LEFT'] == bm_thal
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You can also iterate over all brain structures in a brain model:
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>>> for name, slc, bm in bm_full.iter_structures(): ... # doctest: +SKIP
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>>> for name, slc, bm in bm_full.iter_structures(): ...
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In this case there will be two iterations, namely:
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('CIFTI_STRUCTURE_CORTEX_LEFT', slice(0, <size of cortex mask>), bm_cortex)
@@ -93,23 +93,23 @@
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... ('surface_parcel', bm_cortex[:100]), # contains first 100 cortical vertices
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... ('volume_parcel', bm_thal), # contains thalamus
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... ('combined_parcel', bm_full[[1, 8, 10, 120, 127]) # contains selected voxels/vertices
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... ]) # doctest: +SKIP
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... ])
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Time series are represented by their starting time (typically 0), step size
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(i.e. sampling time or TR), and number of elements:
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>>> series = cifti2.SeriesAxis(start=0, step=100, size=5000) # doctest: +SKIP
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>>> series = cifti2.SeriesAxis(start=0, step=100, size=5000)
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So a header for fMRI data with a TR of 100 ms covering the left cortex and thalamus with
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5000 timepoints could be created with
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>>> cifti2.Cifti2Header.from_axes((series, bm_cortex + bm_thal)) # doctest: +SKIP
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>>> cifti2.Cifti2Header.from_axes((series, bm_cortex + bm_thal))
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Similarly the curvature and cortical thickness on the left cortex could be stored using a header
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like:
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>>> cifti2.Cifti2Header.from_axes((cifti.ScalarAxis(['curvature', 'thickness'],
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... bm_cortex)) # doctest: +SKIP
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... bm_cortex))
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"""
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import numpy as np
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from . import cifti2

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