def test_AFQ_custom_tract():
"""
Test whether AFQ can use tractography from
custom_tractography_bids_filters
"""
_, bids_path, sub_path = get_temp_hardi()
afd.fetch_stanford_hardi_tractography()
bundle_names = ["SLF", "ARC", "CST", "FP"]
# move subsampled tractography into bids folder
os.rename(
op.join(
op.expanduser('~'),
'AFQ_data',
'stanford_hardi_tractography',
'tractography_subsampled.trk'),
op.join(
sub_path,
'subsampled_tractography.trk'
)
)
my_afq = api.AFQ(
bids_path,
dmriprep='vistasoft',
bundle_info=bundle_names,
custom_tractography_bids_filters={
"suffix": "tractography",
"scope": "vistasoft"
})
my_afq.get_streamlines()
#
# The top level directory is our overall bids dataset folder. In most
# cases, this folder will include a `raw` folder that will contain the
# raw data. In this case, we do not include the raw folder and only have
# the derivatives folder that contains the outputs of preprocessing the data.
# In this case, one folder containing Freesurfer derivatives and another
# folder containing the DWI data that has been preprocessed with Vistasoft.
# pyAFQ provides facilities to segment tractography results obtained
# using other software. For example, we often use
# `qsiprep <https://qsiprep.readthedocs.io/en/latest/>`_ to preprocess
# our data and reconstruct tractographies with software such as
# `MRTRIX <https://www.mrtrix.org/>`_. Here, we will demonstrate how to use
# these reconstructions in the pyAFQ segmentation and tractometry pipeline
# We fetch this data and add it as a separate derivatives folder
afd.fetch_stanford_hardi_tractography()
bids_path = op.join(op.expanduser('~'), 'AFQ_data', 'stanford_hardi')
tractography_path = op.join(bids_path, 'derivatives', 'my_tractography')
sub_path = op.join(tractography_path, 'sub-01', 'ses-01', 'dwi')
os.makedirs(sub_path, exist_ok=True)
os.rename(
op.join(op.expanduser('~'), 'AFQ_data', 'stanford_hardi_tractography',
'full_segmented_cleaned_tractography.trk'),
op.join(sub_path, 'sub-01_ses-01-dwi_tractography.trk'))
afd.to_bids_description(
tractography_path, **{
"Name": "my_tractography",
"PipelineDescription": {