pyAFQ 2.0__tar.gz → 2.0.1__tar.gz

{pyafq-2.0 → pyafq-2.0.1}/AFQ/api/bundle_dict.py

@@ -722,8 +722,10 @@ class BundleDict(MutableMapping):
         If there are bundles in bundle_info with the 'space' attribute
         set to 'subject', their images (all ROIs and probability maps)
         will be resampled to the affine and shape of this image.
+        If None, resamples to DWI. Be careful if you use this,
+        that this is the correct choice.
         If False, no resampling will be done.
-        Default: None
+        Default: False
 
     keep_in_memory : bool, optional
         Whether, once loaded, all ROIs and probability maps will stay

{pyafq-2.0 → pyafq-2.0.1}/AFQ/api/participant.py

@@ -156,7 +156,7 @@ class ParticipantAFQ(object):
 
     def export_up_to(self, attr_name="help"):
         f"""
-        Export all derivatives necessary for a specific output.
+        Export all derivatives up to, but not including, the specified output.
         To print a list of available outputs,
         call export_up_to without arguments.
         {valid_exports_string}

{pyafq-2.0 → pyafq-2.0.1}/AFQ/api/utils.py

@@ -1,8 +1,8 @@
 import contextlib
 from importlib import import_module
 from AFQ.viz.utils import viz_import_msg_error
+from AFQ.utils.docstring_parser import parse_numpy_docstring
 import pimms
-from funcargparse import FuncArgParser
 import logging
 import warnings
 
@@ -23,18 +23,31 @@ set_sft_logger_level(logging.CRITICAL)
 
 task_modules = ["data", "mapping", "segmentation", "tractography", "viz"]
 
-methods_descriptors = {}
-methods_sections = {}
+methods_descriptors = {
+    "dwi_data_file": "Path to DWI data file",
+    "bval_file": "Path to bval file",
+    "bvec_file": "Path to bvec file",
+    "output_dir": "Path to output directory",
+    "best_scalar": "Go-to scalar for visualizations",
+    "base_fname": "Base file name for outputs",
+}
+methods_sections = {
+    "dwi_data_file": "data",
+    "bval_file": "data",
+    "bvec_file": "data",
+    "output_dir": "data",
+    "best_scalar": "tractography",
+    "base_fname": "data",
+}
 kwargs_descriptors = {}
 for task_module in task_modules:
     kwargs_descriptors[task_module] = {}
     for calc_obj in import_module(
             f"AFQ.tasks.{task_module}").__dict__.values():
         if isinstance(calc_obj, pimms.calculation.Calc):
-            docstr_parser = FuncArgParser()
-            docstr_parser.setup_args(calc_obj.function)
+            docstr_parsed = parse_numpy_docstring(calc_obj.function)
             if len(calc_obj.efferents) > 1:
-                eff_descs = docstr_parser.description.split(",")
+                eff_descs = docstr_parsed["description"].split(",")
                 if len(eff_descs) != len(calc_obj.efferents):
                     raise NotImplementedError((
                         "If calc method has mutliple outputs, "
@@ -56,10 +69,10 @@ for task_module in task_modules:
             else:
                 methods_descriptors[
                     calc_obj.efferents[0]] =\
-                    docstr_parser.description
+                    docstr_parsed["description"]
                 methods_sections[calc_obj.efferents[0]] =\
                     task_module
-            for arg, info in docstr_parser.unfinished_arguments.items():
+            for arg, info in docstr_parsed["arguments"].items():
                 if "help" in info:
                     default = info["default"] if "default" in info else None
                     kwargs_descriptors[task_module][arg] = dict(

{pyafq-2.0 → pyafq-2.0.1}/AFQ/data/fetch.py

@@ -405,6 +405,8 @@ def read_resample_roi(roi, resample_to=None, threshold=False):
     nibabel image class instance that contains the binary ROI resampled into
     the requested space.
     """
+    logger = logging.getLogger('AFQ')
+
     if isinstance(roi, str):
         roi = nib.load(roi)
 
@@ -414,7 +416,11 @@ def read_resample_roi(roi, resample_to=None, threshold=False):
     if isinstance(resample_to, str):
         resample_to = nib.load(resample_to)
 
-    if resample_to is False or np.allclose(resample_to.affine, roi.affine):
+    if resample_to is False:
+        return roi
+
+    if np.allclose(resample_to.affine, roi.affine):
+        logger.info("Resampling skipped as affines already match.")
         return roi
 
     as_array = resample(

{pyafq-2.0 → pyafq-2.0.1}/AFQ/recognition/criteria.py

@@ -334,6 +334,21 @@ def run_bundle_rec_plan(
         mapping,
         img.affine,
         apply_to_recobundles=True))
+
+    def check_space(roi):
+        if not np.allclose(img.affine, roi.affine):
+            logger.warning(
+                "Resampling set to False in case where affines "
+                "do not match. This is likely due to subject space ROIs"
+                " not being in the right space. This found for bundle "
+                f"{bundle_name}")
+
+    apply_to_roi_dict(
+        bundle_def,
+        check_space,
+        dry_run=True,
+        apply_to_prob_map=True)
+
     apply_to_roi_dict(
         bundle_def,
         lambda roi_img: nib.Nifti1Image(

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tasks/data.py

@@ -86,8 +86,8 @@ def get_data_gtab(dwi_data_file, bval_file, bvec_file, min_bval=None,
         bvals = bvals[valid_b]
         bvecs = bvecs[valid_b]
     gtab = dpg.gradient_table(
-        bvals, bvecs,
-        b0_threshold=b0_threshold)
+        bvals = bvals, bvecs = bvecs,
+        b0_threshold = b0_threshold)
     img = nib.Nifti1Image(data, img.affine)
     return data, gtab, img, img.affine
 
@@ -1081,8 +1081,7 @@ def brain_mask(b0, brain_mask_definition=None):
 
 
 @pimms.calc("bundle_dict", "reg_template", "tmpl_name")
-def get_bundle_dict(segmentation_params,
-                    brain_mask, b0,
+def get_bundle_dict(brain_mask, b0,
                     bundle_info=None, reg_template_spec="mni_T1",
                     reg_template_space_name="mni"):
     """
@@ -1157,6 +1156,9 @@ def get_bundle_dict(segmentation_params,
             bundle_info,
             resample_to=reg_template)
 
+    if bundle_dict.resample_subject_to is None:
+        bundle_dict.resample_subject_to = b0
+
     return bundle_dict, reg_template, reg_template_space_name
 
 

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tasks/segmentation.py

@@ -80,6 +80,11 @@ def segment(data_imap, mapping_imap,
             temp_tck, data_imap["dwi"], Space.VOX,
             bbox_valid_check=False)
         is_trx = False
+    if len(tg.streamlines) == 0:
+        raise ValueError(f"There are no streamlines in {streamlines}."
+                         " This is likely due to errors in defining the "
+                         " tractography parameters or the"
+                         " seed/stop masks.")
 
     indices_to_remove, _ = tg.remove_invalid_streamlines()
     if len(indices_to_remove) > 0:
@@ -382,8 +387,9 @@ def get_scalar_dict(data_imap, mapping_imap, scalars=["dti_fa", "dti_md"]):
         List of scalars to use.
         Can be any of: "dti_fa", "dti_md", "dki_fa", "dki_md", "dki_awf",
         "dki_mk". Can also be a scalar from AFQ.definitions.image.
-            Default: For single shell data: ["dti_fa", "dti_md"], 
-        for multi-shell data: ["dki_fa", "dki_md"].
+        Defaults for single shell data to ["dti_fa", "dti_md"],
+        and for multi-shell data to ["dki_fa", "dki_md"].
+        Default: ['dti_fa', 'dti_md']
     """
     # Note: some scalars preprocessing done in plans, before this step
     scalar_dict = {}

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tasks/tractography.py

@@ -351,6 +351,8 @@ def gpu_tractography(data_imap, tracking_params, fodf, seed, stop,
     if tracking_params["directions"] == "boot":
         data = data_imap["data"]
     else:
+        if isinstance(fodf, str):
+            fodf = nib.load(fodf)
         data = fodf.get_fdata()
 
     sphere = tracking_params["sphere"]

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tasks/viz.py

@@ -365,7 +365,7 @@ def init_viz_backend(viz_backend_spec="plotly_no_gif",
         generating GIFs in a headless environment. Default: False
     viz_backend_spec : str, optional
         Which visualization backend to use.
-        See Visualization Backends page in documentation for details:
+        See Visualization Backends page in documentation for details
         https://tractometry.org/pyAFQ/usage/viz_backend.html
         One of {"fury", "plotly", "plotly_no_gif"}.
         Default: "plotly_no_gif"

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tests/test_api.py

@@ -32,7 +32,7 @@ import AFQ.utils.streamlines as aus
 import AFQ.utils.bin as afb
 from AFQ.definitions.mapping import SynMap, AffMap, SlrMap, IdentityMap
 from AFQ.definitions.image import (RoiImage, PFTImage, ImageFile,
-                                   TemplateImage, LabelledImageFile)
+                                   TemplateImage)
 
 
 def touch(fname, times=None):

{pyafq-2.0 → pyafq-2.0.1}/AFQ/tractography/gputractography.py

@@ -141,10 +141,12 @@ def gpu_track(data, gtab, seed_img, stop_img,
         step_size,
         0.25,  # relative peak threshold
         radians(45),  # min separation angle
-        data.astype(np.float64), H.astype(np.float64), R.astype(np.float64),
+        np.ascontiguousarray(data).astype(np.float64),
+        H.astype(np.float64), R.astype(np.float64),
         delta_b.astype(np.float64), delta_q.astype(np.float64),
-        b0s_mask.astype(np.int32), stop_data.astype(
-            np.float64), sampling_matrix.astype(np.float64),
+        b0s_mask.astype(np.int32),
+        np.ascontiguousarray(stop_data).astype(np.float64),
+        sampling_matrix.astype(np.float64),
         sphere.vertices.astype(np.float64), sphere.edges.astype(np.int32),
         ngpus=ngpus, rng_seed=0)
 
@@ -162,7 +164,7 @@ def gpu_track(data, gtab, seed_img, stop_img,
         # Will resize by a factor of 2 if these are exceeded
         sl_len_guess = 100
         sl_per_seed_guess = 3
-        n_sls_guess = sl_per_seed_guess * len(seeds.shape[0])
+        n_sls_guess = sl_per_seed_guess * seeds.shape[0]
 
         # trx files use memory mapping
         trx_file = TrxFile(
@@ -193,7 +195,7 @@ def gpu_track(data, gtab, seed_img, stop_img,
                 # TRX uses memmaps here
                 trx_file.streamlines._data[sls_data_idx:new_sls_data_idx] = sls._data
                 trx_file.streamlines._offsets[offsets_idx:
-                                              new_offsets_idx] = offsets_idx + sls._offsets
+                                              new_offsets_idx] = sls_data_idx + sls._offsets
                 trx_file.streamlines._lengths[offsets_idx:new_offsets_idx] = sls._lengths
 
                 offsets_idx = new_offsets_idx

{pyafq-2.0 → pyafq-2.0.1}/AFQ/utils/bin.py

@@ -4,13 +4,13 @@ import platform
 import os.path as op
 
 from argparse import ArgumentParser
-from funcargparse import FuncArgParser
 
 from AFQ.definitions.image import *  # interprets masks loaded from toml
 from AFQ.definitions.mapping import *  # interprets mappings loaded from toml
 from AFQ.api.bundle_dict import *  # interprets bundle_dicts loaded from toml
 from AFQ.definitions.utils import Definition
 from AFQ.api.utils import kwargs_descriptors
+from AFQ.utils.docstring_parser import parse_numpy_docstring
 
 import nibabel as nib  # allows users to input nibabel objects
 
@@ -178,11 +178,10 @@ def func_dict_to_arg_dict(func_dict=None, logger=None):
 
     arg_dict = {}
     for name, func in func_dict.items():
-        docstr_parser = FuncArgParser()
-        docstr_parser.setup_args(func)
+        docstr_parsed = parse_numpy_docstring(func)
         if name == "BIDS":
-            arg_dict["AFQ_desc"] = docstr_parser.description
-        for arg, info in docstr_parser.unfinished_arguments.items():
+            arg_dict["AFQ_desc"] = docstr_parsed["description"]
+        for arg, info in docstr_parsed["arguments"].items():
             try:
                 section = name.upper() + "_PARAMS"
                 desc = info['help']

pyafq-2.0.1/AFQ/utils/docstring_parser.py

@@ -0,0 +1,123 @@
+import re
+import inspect
+
+__all__ = ["parse_numpy_docstring"]
+
+
+def _white_space(text):
+    if text is None:
+        return None
+    else:
+        return re.sub(r'[\n\t\s]+', ' ', text).strip()
+
+
+def _split_parameter_blocks(docstring):
+    # First extract just the Parameters section
+    params_section = re.search(
+        r'Parameters\n-+\n(.*?)(?=\n\s*\n|\n-+\n|\Z)',
+        docstring,
+        re.DOTALL
+    )
+    if not params_section:
+        return []
+
+    params_text = params_section.group(1)
+    params_text = re.sub(r'\n-+$', '', params_text)
+    lines = params_text.split('\n')
+
+    # Find base indentation (minimum indent of parameter lines)
+    base_indent = float('inf')
+    for line in lines:
+        if re.match(r'\S', line):
+            indent = len(re.match(r'^\s*', line).group())
+            base_indent = min(base_indent, indent)
+
+    if base_indent == float('inf'):
+        return []
+
+    # Split into blocks
+    param_blocks = []
+    current_block = []
+
+    for line in lines:
+        line_indent = len(re.match(r'^\s*', line).group())
+        if line_indent == base_indent and re.match(r'\S', line):
+            if current_block:
+                param_blocks.append('\n'.join(current_block))
+                current_block = []
+        current_block.append(line)
+
+    if current_block:
+        param_blocks.append('\n'.join(current_block))
+
+    return param_blocks
+
+
+def parse_numpy_docstring(docstring):
+    """
+    Parse a NumPy-style docstring into parameter information.
+
+    Returns:
+        dict: {
+            "description": str (first section of docstring),
+            "arguments": {
+                param_name: {
+                    "help": str (description),
+                    "metavar": str (type),
+                    "default": any (default value)
+                }
+            }
+        }
+    """
+    if callable(docstring):
+        docstring = inspect.getdoc(docstring)
+
+    if not docstring:
+        return {"description": "", "arguments": {}}
+
+    # Find the description section
+    sections = re.split(r'\n\s*\n', docstring.strip())
+    description = sections[0].strip()
+
+    # Find the parameters section
+    param_blocks = _split_parameter_blocks(docstring)
+    params = {}
+
+    for block in param_blocks:
+        # Split into (param: value) and description
+        parts = block.split('\n', maxsplit=1)
+        if len(parts) == 0:
+            continue
+
+        # Parse the (param: value)
+        header_match = re.match(
+            r'(\w+)\s*:\s*([^,\n]+)(?:,\s*optional)?',
+            parts[0].strip()
+        )
+
+        if not header_match:
+            continue
+
+        name, type_info = header_match.groups()
+        desc = parts[1].strip() if len(parts) > 1 else ''
+
+        # Parse the description
+        default = None
+        default_match = re.search(r'[Dd]efault:\s*([^\n]+)', desc)
+        if default_match:
+            default = default_match.group(1).strip(" .")
+            try:
+                default = eval(default)
+            except:
+                default = _white_space(default)
+
+        params[name] = {
+            "help": _white_space(desc),
+            "metavar": _white_space(type_info),
+            "default": default
+        }
+
+    return {
+        "description": _white_space(description),
+        "arguments": params
+    }

{pyafq-2.0 → pyafq-2.0.1}/AFQ/utils/path.py

@@ -70,6 +70,9 @@ def apply_cmd_to_afq_derivs(
             "dependent_on must be one of "
             "None, 'track', 'recog', 'prof'."))
 
+    if cmd == "rm" or cmd == "cp":
+        cmd = cmd + " -r"
+
     if not op.exists(derivs_dir):
         return
 
@@ -92,23 +95,23 @@ def apply_cmd_to_afq_derivs(
                 os.system(f"{cmd} {full_path} {suffix}")
         elif os.path.isdir(full_path):
             if dependent_on is None:
-                os.system(f"{cmd} -r {full_path} {suffix}")
+                os.system(f"{cmd} {full_path} {suffix}")
             else:
                 if filename == "ROIs" and "rec" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "stats" and "rec" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "tractography" and "trk" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "models" and "dwi" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "bundles" and "rec" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "viz_bundles" and "rec" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "viz_core_bundles" and \
                         "prof" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")
                 if filename == "tract_profile_plots" and \
                         "prof" in dependent_on_list:
-                    os.system(f"{cmd} -r {full_path} {suffix}")
+                    os.system(f"{cmd} {full_path} {suffix}")

{pyafq-2.0 → pyafq-2.0.1}/AFQ/version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.0'
-__version_tuple__ = version_tuple = (2, 0)
+__version__ = version = '2.0.1'
+__version_tuple__ = version_tuple = (2, 0, 1)

{pyafq-2.0 → pyafq-2.0.1}/AFQ/viz/utils.py

@@ -261,6 +261,10 @@ class PanelFigure():
         self.fig.canvas.draw()
         for (y_coord, x_coord, subplot_label_pos, label_text, kwargs) in \
                 self.panel_label_queue:
+            if isinstance(x_coord, slice):
+                x_coord = x_coord.start
+            if isinstance(y_coord, slice):
+                y_coord = y_coord.start
             x_fig_pos = x_coord / self.grid.ncols
             y_fig_pos = 1.0 - (y_coord / self.grid.nrows)
             self.fig.text(

{pyafq-2.0 → pyafq-2.0.1}/CHANGES.rst

@@ -1,3 +1,37 @@
+2.0.1 (May 15, 2025)
+====================
+Minor Fixes to VOF, ROI dists, baby BD primary axis filtering, import_tract
+with trx files. Increase in number of examples in docs.
+  * [DOC] update broken references (#90)
+  * Add track, segment, cleaning explanation (#87)
+  * [DOC] How to Export examples (#86)
+  * [DOC] Add GPU, clobber docs (#82)
+  * [DOC] ParticipantAFQ example (#83)
+  * Small docs/viz tool improvements (#62)
+  * [ENH] Make Subject Space ROIs Resample By Default (#72)
+  * Upgrade DIPY dependency. (#76)
+  * Remove funcargparser dependency, replace with extreme regex (#80)
+  * RF: Better error handling. (#68)
+  * update reference in example (#75)
+  * [FIX] recently added typo in pyAFQ GPU integration (#74)
+  * DOC: Adds an example of tract profile visualization with "glass brain". (#67)
+  * remove dependencies; clarify <3.13 for now (#66)
+  * Loosen skimage dependency pin to be larger than 0.14.2 (#61)
+  * [FIX] make import_tract work better with TRX files (#54)
+  * Remove numpy version restrictions (#53)
+  * Further tweaks to new file system (#50)
+  * [FIX] change helvetica-bold to helvetica in pyAFQ plotting library (#49)
+  *  (#48)
+  * [ENH/FIX] Pyafq file outputs more folders, more BIDS (#43)
+  * [ENH] Include custom ODFs (#33)
+  * [ENH] update to numpy 2 (#46)
+  * [ENH] update to 3.12 (#45)
+  * [FIX] fix VOF (#29)
+  * [DOC] added singularity build and usage (#28)
+  * [ENH] Use Distance Transform for Include/Exclude Distance calculation; fix ROI dists (#25)
+  * DOC: Document the significance of ROIS order in BundleDict (#27)
+  * [FIX] update baby BD to new primary axis api (#26)
+
 2.0 (February 25, 2025)
 =======================
 This is a major version release, which includes support for Python 3.12 and

{pyafq-2.0/pyAFQ.egg-info → pyafq-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pyAFQ
-Version: 2.0
+Version: 2.0.1
 Summary: pyAFQ: Automated Fiber Quantification ... in Python
 Home-page: https://tractometry.github.io/pyAFQ
 Download-URL: https://github.com/tractometry/pyAFQ
@@ -21,7 +21,7 @@ Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: scikit_image>=0.14.2
-Requires-Dist: dipy<1.11.0,>=1.10.0
+Requires-Dist: dipy<1.12.0,>=1.11.0
 Requires-Dist: pandas
 Requires-Dist: pybids>=0.16.2
 Requires-Dist: templateflow>=0.8
@@ -31,7 +31,6 @@ Requires-Dist: trx-python
 Requires-Dist: ray
 Requires-Dist: toml>=0.10.0
 Requires-Dist: setuptools_scm[toml]<5.1.0,>=3.4.0
-Requires-Dist: funcargparse>=0.2.0
 Requires-Dist: plotly==5.12.0
 Requires-Dist: kaleido==0.2.1
 Requires-Dist: imageio>=2.0.0
@@ -104,6 +103,7 @@ Requires-Dist: s3bids>=0.1.7; extra == "all"
 Requires-Dist: s3fs; extra == "all"
 Requires-Dist: boto3>=1.14.0; extra == "all"
 Dynamic: download-url
+Dynamic: license-file
 
 # pyAFQ
 Automated Fiber Quantification ... in Python.

pyafq-2.0.1/docs/source/howto/usage/cleaning_params.rst

@@ -0,0 +1,35 @@
+==========================
+Cleaning Parameters
+==========================
+
+This page documents the configuration options for controlling
+bundle cleaning in pyAFQ. These parameters can be set in your
+configuration file or passed as arguments when using the API.
+Note that this goes inside of segmentation_params.
+
+Example Usage
+=============
+
+.. code-block:: python
+
+    from AFQ.api.group import GroupAFQ
+    import AFQ.data.fetch as afd
+    import os.path as op
+
+    afd.organize_stanford_data()
+
+    myafq = GroupAFQ(
+        bids_path=op.join(afd.afq_home, 'stanford_hardi'),
+        preproc_pipeline='vistasoft',
+        segmentation_params=dict(
+            cleaning_params=dict(
+                distance_threshold=5,
+                length_threshold=5,  # More lenient cleaning
+            ))
+        )
+
+Cleaning Parameter Reference
+================================
+
+.. autofunction:: AFQ.recognition.cleaning.clean_bundle
+   :noindex:

{pyafq-2.0 → pyafq-2.0.1}/docs/source/howto/usage/index.rst

@@ -13,3 +13,6 @@ How to use `pyAFQ`
     docker
     methods
     image
+    tractography_params
+    segmentation_params
+    cleaning_params

pyafq-2.0.1/docs/source/howto/usage/segmentation_params.rst

@@ -0,0 +1,33 @@
+==========================
+Segmentation Parameters
+==========================
+
+This page documents the configuration options for controlling
+tractography in pyAFQ. These parameters can be set in your
+configuration file or passed as arguments when using the API.
+
+Example Usage
+=============
+
+.. code-block:: python
+
+    from AFQ.api.group import GroupAFQ
+    import AFQ.data.fetch as afd
+    import os.path as op
+
+    afd.organize_stanford_data()
+
+    myafq = GroupAFQ(
+        bids_path=op.join(afd.afq_home, 'stanford_hardi'),
+        preproc_pipeline='vistasoft',
+        segmentation_params=dict(
+            dist_to_waypoint=10,
+            dist_to_atlas=10)
+        )
+
+
+Segmentation Parameter Reference
+================================
+
+.. autofunction:: AFQ.recognition.recognize.recognize
+   :noindex:

pyafq-2.0.1/docs/source/howto/usage/tractography_params.rst

@@ -0,0 +1,34 @@
+==========================
+Tractography Parameters
+==========================
+
+This page documents the configuration options for controlling
+tractography in pyAFQ. These parameters can be set in your configuration file
+or passed as arguments when using the API.
+
+Example Usage
+=============
+
+.. code-block:: python
+
+    from AFQ.api.group import GroupAFQ
+    import AFQ.data.fetch as afd
+    import os.path as op
+
+    afd.organize_stanford_data()
+
+    myafq = GroupAFQ(
+        bids_path=op.join(afd.afq_home, 'stanford_hardi'),
+        preproc_pipeline='vistasoft',
+        tracking_params=dict(
+            n_seeds=25000,
+            random_seeds=True,
+            rng_seed=2025,
+            trx=True)
+        )
+
+Tractography Parameter Reference
+================================
+
+.. autofunction:: AFQ.tractography.tractography.track
+   :noindex: