Using RecoBundles for bundle recognition#
For bundle recognition, pyAFQ defaults to use the waypoint ROI approach described in [Yeatman2012]. However, as an alternative approach, pyAFQ also supports using the RecoBundles algorithm [Garyfallidis2017], which uses an atlas of bundles in streamlines. This example shows how to use RecoBundles for bundle recognition.
The code closely resembles the code used in sphx_glr_tutorial_examples_plot_001-plot_afq_api.py.
import os.path as op
import AFQ.data.fetch as afd
from AFQ.api.group import GroupAFQ
import AFQ.api.bundle_dict as abd
afd.organize_stanford_data(clear_previous_afq="track")
tracking_params = dict(n_seeds=25000,
random_seeds=True,
rng_seed=42)
/opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
from .autonotebook import tqdm as notebook_tqdm
2026-05-26 22:58:03,320 INFO util.py:154 -- Missing packages: ['ipywidgets']. Run `pip install -U ipywidgets`, then restart the notebook server for rich notebook output.
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
Cell In[1], line 6
2 import AFQ.data.fetch as afd
3 from AFQ.api.group import GroupAFQ
4 import AFQ.api.bundle_dict as abd
5
----> 6 afd.organize_stanford_data(clear_previous_afq="track")
7
8 tracking_params = dict(n_seeds=25000,
9 random_seeds=True,
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/AFQ/data/fetch.py:1819, in organize_stanford_data(path, clear_previous_afq)
1817 # fetches data for first subject and session
1818 logger.info("fetching Stanford HARDI data")
-> 1819 dpd.fetch_stanford_hardi()
1821 if path is None:
1822 if not op.exists(afq_home):
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/dipy/data/fetcher.py:494, in _make_fetcher.<locals>.fetcher(include_optional)
491 continue
492 files[str(n)] = (baseurl + f, md5_list[i] if md5_list is not None else None)
--> 494 fetch_data(files, folder, data_size=data_size, use_headers=use_headers)
496 if msg is not None:
497 logger.info(msg)
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/dipy/testing/decorators.py:201, in warning_for_keywords.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
194 # Check if the current version is within the warning range
195 if (
196 version.parse(from_version)
197 <= version.parse(current_version)
198 <= version.parse(until_version)
199 ):
200 # Convert positional to keyword arguments and issue a warning
--> 201 return convert_positional_to_keyword(func, args, kwargs)
203 # If the version is greater than the until_version,
204 # pass the arguments as they are
205 elif version.parse(current_version) > version.parse(until_version):
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/dipy/testing/decorators.py:192, in warning_for_keywords.<locals>.decorator.<locals>.wrapper.<locals>.convert_positional_to_keyword(func, args, kwargs)
182 warnings.warn(
183 f"Pass {positionally_passed_kwonly_args} as keyword args. "
184 f"From version {until_version} passing these as positional "
(...) 187 stacklevel=3,
188 )
190 return func(*positional_args, **corrected_kwargs)
--> 192 return func(*args, **kwargs)
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/dipy/data/fetcher.py:397, in fetch_data(files, folder, data_size, use_headers, raise_on_error)
395 logger.info(f"From: {url}")
396 try:
--> 397 _get_file_data(fullpath, url, use_headers=use_headers, stored_md5=md5)
398 successful_downloads += 1
399 except (FetcherError, Exception) as e:
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/site-packages/dipy/data/fetcher.py:262, in _get_file_data(fname, url, use_headers, timeout, max_retries, stored_md5)
260 with open(fname, "wb") as data:
261 if response_size is None:
--> 262 copyfileobj(opener, data)
263 else:
264 copyfileobj_withprogress(opener, data, response_size)
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/shutil.py:203, in copyfileobj(fsrc, fdst, length)
201 fsrc_read = fsrc.read
202 fdst_write = fdst.write
--> 203 while buf := fsrc_read(length):
204 fdst_write(buf)
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/http/client.py:478, in HTTPResponse.read(self, amt)
475 return b""
477 if self.chunked:
--> 478 return self._read_chunked(amt)
480 if amt is not None and amt >= 0:
481 if self.length is not None and amt > self.length:
482 # clip the read to the "end of response"
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/http/client.py:608, in HTTPResponse._read_chunked(self, amt)
605 self.chunk_left = chunk_left - amt
606 break
--> 608 value.append(self._safe_read(chunk_left))
609 if amt is not None:
610 amt -= chunk_left
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/http/client.py:648, in HTTPResponse._safe_read(self, amt)
641 """Read the number of bytes requested.
642
643 This function should be used when <amt> bytes "should" be present for
644 reading. If the bytes are truly not available (due to EOF), then the
645 IncompleteRead exception can be used to detect the problem.
646 """
647 cursize = min(amt, _MIN_READ_BUF_SIZE)
--> 648 data = self.fp.read(cursize)
649 if len(data) >= amt:
650 return data
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/socket.py:719, in SocketIO.readinto(self, b)
717 raise OSError("cannot read from timed out object")
718 try:
--> 719 return self._sock.recv_into(b)
720 except timeout:
721 self._timeout_occurred = True
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/ssl.py:1304, in SSLSocket.recv_into(self, buffer, nbytes, flags)
1300 if flags != 0:
1301 raise ValueError(
1302 "non-zero flags not allowed in calls to recv_into() on %s" %
1303 self.__class__)
-> 1304 return self.read(nbytes, buffer)
1305 else:
1306 return super().recv_into(buffer, nbytes, flags)
File /opt/hostedtoolcache/Python/3.13.13/x64/lib/python3.13/ssl.py:1138, in SSLSocket.read(self, len, buffer)
1136 try:
1137 if buffer is not None:
-> 1138 return self._sslobj.read(len, buffer)
1139 else:
1140 return self._sslobj.read(len)
KeyboardInterrupt:
Defining the segmentation params#
We also refer to bundle recognition as the “segmentation” of the tractogram.
Parameters of this process are set through a dictionary input to the
segmentation_params argument of the GroupAFQ object. In this case, we
use abd.reco_bd(16), which tells pyAFQ to use the RecoBundles
algorithm for bundle recognition. This uses 16 bundles, there is also
an atlas abd.reco_bd(80) which uses 80 bundles.
myafq = GroupAFQ(
output_dir=op.join(afd.afq_home, 'stanford_hardi', 'derivatives',
'recobundles'),
bids_path=op.join(afd.afq_home, 'stanford_hardi'),
# Set the algorithm to use RecoBundles for bundle recognition:
bundle_info=abd.reco_bd(16),
dwi_preproc_pipeline='vistasoft',
t1_preproc_pipeline='freesurfer',
tracking_params=tracking_params,
viz_backend_spec='plotly_no_gif')
fig_files = myafq.export_all()
References:#
.. [Garyfallidis2017] Garyfallidis, Eleftherios, Marc-Alexandre Côté, Francois Rheault, Jasmeen Sidhu, Janice Hau, Laurent Petit, David Fortin, Stephen Cunanne, and Maxime Descoteaux. 2017.“Recognition of White Matter Bundles Using Local and Global Streamline-Based Registration and Clustering.”NeuroImage 170: 283-295.