How to segment out only some bundles#
The pyAFQ software can be configured to find all of its default set of white matter pathways, or bundles. Alternatively, it can be configured to find only some bundles. This example shows how to track and recognize only certain bundles that you are interested in, though note that ARC, pARC and VOF are all also part of the set of bundles that are segmented per default.
import AFQ.api.bundle_dict as abd
import AFQ.data.fetch as afd
from AFQ.api.group import GroupAFQ
from AFQ.definitions.image import RoiImage
import AFQ.utils.streamlines as aus
import os.path as op
afd.organize_stanford_data(clear_previous_afq="track")
bundle_names = [
"Left Arcuate", "Right Arcuate",
"Left Posterior Arcuate", "Right Posterior Arcuate",
"Left Vertical Occipital", "Right Vertical Occipital"]
bundle_dict = abd.default_bd()[bundle_names]
myafq = GroupAFQ(
op.join(afd.afq_home, 'stanford_hardi'),
bundle_info=bundle_dict,
dwi_preproc_pipeline='vistasoft',
t1_preproc_pipeline='freesurfer',
tracking_params={
"n_seeds": 50000,
"random_seeds": True,
"seed_mask": RoiImage(use_waypoints=True, use_endpoints=True),
}
)
for b_name in bundle_names:
b_len = len(aus.SegmentedSFT.fromfile(myafq.export("bundles")[
"01"]).get_bundle(b_name))
if b_len < 1:
raise ValueError(f"{b_name} not found")
myafq.export("all_bundles_figure")["01"][0]
2026-05-26 22:59:12,255 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 9
5 import AFQ.utils.streamlines as aus
6
7 import os.path as op
8
----> 9 afd.organize_stanford_data(clear_previous_afq="track")
10
11 bundle_names = [
12 "Left Arcuate", "Right Arcuate",
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: