pyAFQ 3.1__tar.gz → 3.2__tar.gz

{pyafq-3.1 → pyafq-3.2}/AFQ/api/bundle_dict.py

@@ -300,6 +300,7 @@ def default_bd():
                     templates["SLF_roi1_L"],
                     templates["IFO_roi1_L"],
                     templates["pARC_xroi1_L"],
+                    templates["TPSPL_roi1_L"],
                 ],
                 "space": "template",
                 "start": templates["pARC_L_start"],
@@ -316,6 +317,7 @@ def default_bd():
                     templates["SLF_roi1_R"],
                     templates["IFO_roi1_R"],
                     templates["pARC_xroi1_R"],
+                    templates["TPSPL_roi1_R"],
                 ],
                 "space": "template",
                 "start": templates["pARC_R_start"],
@@ -325,6 +327,44 @@ def default_bd():
                 "length": {"min_len": 30},
                 "primary_axis": "I/S",
             },
+            "Left Temporo-parietal": {
+                "cross_midline": False,
+                "include": [
+                    templates["SLFt_roi2_L"],
+                    templates["TPSPL_roi1_L"],
+                ],
+                "exclude": [
+                    templates["SLF_roi1_L"],
+                    templates["IFO_roi1_L"],
+                    templates["pARC_xroi1_L"],
+                ],
+                "space": "template",
+                "start": templates["pARC_L_start"],
+                "end": templates["pARC_L_end"],
+                "Left Arcuate": {"overlap": 20},
+                "Left Optic Radiation": {"core": "Right"},
+                "length": {"min_len": 30},
+                "primary_axis": "I/S",
+            },
+            "Right Temporo-parietal": {
+                "cross_midline": False,
+                "include": [
+                    templates["SLFt_roi2_R"],
+                    templates["TPSPL_roi1_R"],
+                ],
+                "exclude": [
+                    templates["SLF_roi1_R"],
+                    templates["IFO_roi1_R"],
+                    templates["pARC_xroi1_R"],
+                ],
+                "space": "template",
+                "start": templates["pARC_R_start"],
+                "end": templates["pARC_R_end"],
+                "Right Arcuate": {"overlap": 20},
+                "Right Optic Radiation": {"core": "Left"},
+                "length": {"min_len": 30},
+                "primary_axis": "I/S",
+            },
             "Left Vertical Occipital": {
                 "cross_midline": False,
                 "space": "template",

{pyafq-3.1 → pyafq-3.2}/AFQ/data/fetch.py

@@ -783,6 +783,8 @@ template_fnames = [
     "VOF_xroi1_R.nii.gz",
     "VOF_xroi2_L.nii.gz",
     "VOF_xroi2_R.nii.gz",
+    "TPSPL_roi1_L.nii.gz",
+    "TPSPL_roi1_R.nii.gz",
 ]
 
 
@@ -903,6 +905,8 @@ template_remote_fnames = [
     "62582596",
     "62582599",
     "62582602",
+    "64928463",
+    "64928466",
 ]
 
 
@@ -1024,6 +1028,8 @@ template_md5_hashes = [
     "0cda34ce714759bad909fcf9051f3d64",
     "6b65a5e178853e993f52b438ffb0f6c6",
     "e36f5adf08eb3efd5849397f0f8ef6a4",
+    "4418a1277ff768a5752368edda2bbcac",
+    "44db3c4b841bca2e8b56ef4f650fa3d5",
 ]
 
 fetch_templates = _make_reusable_fetcher(

{pyafq-3.1 → pyafq-3.2}/AFQ/models/dki.py

@@ -11,14 +11,6 @@ import AFQ.utils.models as ut
 __all__ = ["fit_dki", "predict"]
 
 
-def _fit(gtab, data, mask=None, return_S0_hat=False):
-    dkimodel = dki.DiffusionKurtosisModel(gtab, return_S0_hat=return_S0_hat)
-    return dkimodel.fit(
-        data,
-        mask=mask,
-    )
-
-
 def fit_dki(
     data_files,
     bval_files,

{pyafq-3.1 → pyafq-3.2}/AFQ/models/msmt.py

@@ -28,12 +28,6 @@ def _fit(self, data, mask=None):
     for i in range(A.shape[0]):
         A[i] /= np.linalg.norm(A[i])
 
-    A_outer = np.empty((n, n, m), dtype=np.float64)
-    for k in range(m):
-        for i in range(n):
-            for j in range(n):
-                A_outer[i, j, k] = A[k, i] * A[k, j]
-
     Q = R.T @ R
 
     A = csr_matrix(A)

{pyafq-3.1 → pyafq-3.2}/AFQ/tasks/data.py

@@ -27,7 +27,6 @@ from AFQ.models.asym_filtering import (
 )
 from AFQ.models.csd import CsdNanResponseError
 from AFQ.models.csd import _fit as csd_fit_model
-from AFQ.models.dki import _fit as dki_fit_model
 from AFQ.models.dti import _fit as dti_fit_model
 from AFQ.models.dti import noise_from_b0
 from AFQ.models.fwdti import _fit as fwdti_fit_model
@@ -315,7 +314,11 @@ def dki_params(brain_mask, gtab, data, citations):
             )
         )
     mask = nib.load(brain_mask).get_fdata()
-    dkf = dki_fit_model(gtab, data, mask=mask, return_S0_hat=True)
+    dkimodel = dpy_dki.DiffusionKurtosisModel(gtab, return_S0_hat=True)
+    dkf = dkimodel.fit(
+        data,
+        mask=mask,
+    )
     meta = dict(
         Description=(
             "Diffusion Coefficient, encoded as a kurtosis tensor representation"
@@ -408,7 +411,9 @@ def msdki_msd(msdki_tf):
     full path to a nifti file containing
     the MSDKI mean signal diffusivity
     """
-    return msdki_tf.msd, {"Description": "Mean Signal Diffusivity"}
+    msd = msdki_tf.msd.copy()
+    msd[msd < 0] = 0
+    return msd, {"Description": "Mean Signal Diffusivity"}
 
 
 @immlib.calc("msdki_msk")
@@ -419,7 +424,10 @@ def msdki_msk(msdki_tf):
     full path to a nifti file containing
     the MSDKI mean signal kurtosis
     """
-    return msdki_tf.msk, {"Description": "Mean Signal Kurtosis"}
+    msk = msdki_tf.msk.copy()
+    msk[msk < 0] = 0
+    msk[msk > 10] = 0
+    return msk, {"Description": "Mean Signal Kurtosis"}
 
 
 @immlib.calc("csd_params")
@@ -1480,7 +1488,13 @@ def get_data_plan(kwargs):
     if "scalars" not in kwargs:
         bvals, _ = read_bvals_bvecs(kwargs["bval_file"], kwargs["bvec_file"])
         if len(dpg.unique_bvals_magnitude(bvals)) > 2:
-            kwargs["scalars"] = ["dki_fa", "dki_md", "dki_kfa", "dki_mk", "t1w_over_b0"]
+            kwargs["scalars"] = [
+                "dti_fa",
+                "dti_md",
+                "t1w_over_b0",
+                "msdki_msd",
+                "msdki_msk",
+            ]
         else:
             kwargs["scalars"] = ["dti_fa", "dti_md", "t1w_over_b0"]
     else:

{pyafq-3.1 → pyafq-3.2}/AFQ/tasks/segmentation.py

@@ -398,14 +398,14 @@ def get_scalar_dict(
         "dki_mk", or other scalars found in AFQ.tasks.data.
         Can also be a scalar from AFQ.definitions.image.
         Finally, can also be "t1w".
-        Defaults for single shell data to ["dti_fa", "dti_md", "t1w"],
-        and for multi-shell data to ["dki_fa", "dki_md", "dki_kfa",
-        "dki_mk", "t1w"].
-        Default: ['dti_fa', 'dti_md', 't1w']
+        Defaults for single shell data to ["dti_fa", "dti_md", "t1w_over_b0"],
+        and for multi-shell data to ["dti_fa", "dti_md", "t1w_over_b0",
+        "msdki_msd", "msdki_msk"].
+        Default: ['dti_fa', 'dti_md', 't1w_over_b0']
     """
-    # Note: some scalars preprocessing done in mapping plan, before this step
+    # Note: some scalars preprocessing done in data plan, before this step
     if scalars is None:
-        scalars = ["dti_fa", "dti_md", "t1w"]
+        scalars = ["dti_fa", "dti_md", "t1w_over_b0"]
     scalar_dict = {}
     for scalar in scalars:
         if isinstance(scalar, str):

{pyafq-3.1 → pyafq-3.2}/AFQ/tasks/structural.py

@@ -2,6 +2,7 @@ import logging
 
 import immlib
 import nibabel as nib
+import numpy as np
 from numba import get_num_threads
 
 from AFQ.definitions.utils import Definition
@@ -90,7 +91,7 @@ def onnx_kwargs(
 
 @immlib.calc("synthseg_model")
 @as_file(suffix="_model-synthseg2_probseg.nii.gz", subfolder="nn")
-def synthseg_model(t1_masked, citations, onnx_kwargs):
+def synthseg_model(t1_file, citations, onnx_kwargs):
     """
     full path to the synthseg2 model segmentations
 
@@ -110,9 +111,9 @@ def synthseg_model(t1_masked, citations, onnx_kwargs):
         "SynthSeg 2.0",
         "Or, provide your own segmentations using PVEImage or PVEImages.",
     )
-    t1_img = nib.load(t1_masked)
+    t1_img = nib.load(t1_file)
     predictions = run_synthseg(ort, t1_img, "synthseg2", onnx_kwargs)
-    return predictions, dict(T1w=t1_masked)
+    return predictions, dict(T1w=t1_file)
 
 
 @immlib.calc("mx_model")
@@ -143,7 +144,7 @@ def mx_model(t1_file, t1w_brain_mask, citations, onnx_kwargs):
 
 @immlib.calc("t1w_brain_mask")
 @as_file(suffix="_desc-T1w_mask.nii.gz")
-def t1w_brain_mask(t1_file, citations, onnx_kwargs, brain_mask_definition=None):
+def t1w_brain_mask(synthseg_model, brain_mask_definition=None):
     """
     full path to a nifti file containing brain mask from T1w image
 
@@ -154,28 +155,27 @@ def t1w_brain_mask(t1_file, citations, onnx_kwargs, brain_mask_definition=None):
         the brain mask, which gets applied before registration to a
         template.
         If you want no brain mask to be applied, use FullImage.
-        If None, use Brainchop Mindgrab model.
+        If None, use Synthseg model.
         Default: None
 
     References
     ----------
-    [1] Masoud, M., Hu, F., & Plis, S. (2023). Brainchop: In-browser MRI
-        volumetric segmentation and rendering. Journal of Open Source
-        Software, 8(83), 5098.
-        https://doi.org/10.21105/joss.05098
+    [1] Billot, Benjamin, et al. "Robust machine learning segmentation
+        for large-scale analysis of heterogeneous clinical brain MRI
+        datasets." Proceedings of the National Academy of Sciences 120.9
+        (2023): e2216399120.
+    [2] Billot, Benjamin, et al. "SynthSeg: Segmentation of brain MRI scans
+        of any contrast and resolution without retraining." Medical image
+        analysis 86 (2023): 102789.
     """
     # Note that any case where brain_mask_definition is not None
-    # is handled in get_data_plan
+    # is handled in get_structural_plan
     # This is just the default
 
-    citations.add("fani2025mindgrab")
-
-    ort = check_onnxruntime(
-        "Mindgrab", "Or, provide your own brain mask using brain_mask_definition."
-    )
-    return run_brainchop(ort, nib.load(t1_file), "mindgrab", onnx_kwargs), dict(
-        T1w=t1_file, model="mindgrab"
-    )
+    predictions = nib.load(synthseg_model)
+    brain_mask = (predictions.get_fdata() > 0).astype(np.uint8)
+    brain_mask_img = nib.Nifti1Image(brain_mask, predictions.affine)
+    return brain_mask_img, dict(SynthsegPredictions=synthseg_model)
 
 
 @immlib.calc("t1_masked")

{pyafq-3.1 → pyafq-3.2}/AFQ/tests/test_api.py

@@ -340,7 +340,7 @@ def test_AFQ_init():
                     dwi_preproc_pipeline="synthetic",
                     participant_labels=participant_labels,
                 )
-                myafq.export("dwi")
+                myafq.export("b0")
 
 
 @pytest.mark.nightly_basic
@@ -990,12 +990,20 @@ def test_AFQ_data_waypoint():
         'suffix="seg", filters={"scope": "freesurfer"},'
         "inclusive_labels=[1, 2]))"
     )
+    bm_def_as_str = (
+        "LabelledImageFile(suffix='seg', "
+        "filters={'scope': 'freesurfer'}, "
+        "exclusive_labels=[0])"
+    )
     config = dict(
         BIDS_PARAMS=dict(
             bids_path=bids_path,
             dwi_preproc_pipeline="vistasoft",
             t1_preproc_pipeline="freesurfer",
         ),
+        STRUCTURAL=dict(
+            brain_mask_definition=bm_def_as_str,
+        ),
         DATA=dict(bundle_info=bundle_dict_as_str),
         TISSUE=dict(pve=pve_as_str),
         SEGMENTATION=dict(

{pyafq-3.1 → pyafq-3.2}/AFQ/tests/test_bundle_dict.py

@@ -20,7 +20,7 @@ def test_BundleDict():
     # test defaults
     afq_bundles = abd.default_bd()
 
-    assert len(afq_bundles) == 20
+    assert len(afq_bundles) == 22
 
     # Arcuate Fasciculus
     afq_bundles = abd.default_bd()["Left Arcuate", "Right Arcuate"]

{pyafq-3.1 → pyafq-3.2}/AFQ/version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '3.1'
-__version_tuple__ = version_tuple = (3, 1)
+__version__ = version = '3.2'
+__version_tuple__ = version_tuple = (3, 2)
 
-__commit_id__ = commit_id = 'gce5c4b5da'
+__commit_id__ = commit_id = 'gd5b3faf6a'

{pyafq-3.1 → pyafq-3.2}/AFQ/viz/altair.py

@@ -138,6 +138,9 @@ def altair_df_to_chart(
         "DKI MK": "",
         "DTI FA": "",
         "DTI MD": " (µm²/ms)",
+        "MSDKI MSD": " (µm²/ms)",
+        "MSDKI MSK": "",
+        "T1W OVER B0": "",
     }
 
     if bundle_list is None:

{pyafq-3.1 → pyafq-3.2}/AFQ/viz/utils.py

@@ -121,8 +121,8 @@ COLOR_DICT = OrderedDict(
         "AF_L": tableau_20[18],
         "Right Arcuate": tableau_20[19],
         "AF_R": tableau_20[19],
-        "Left Posterior Arcuate": tableau_20[14],
-        "Right Posterior Arcuate": tableau_20[15],
+        "Left Posterior Arcuate": (0.0, 0.7, 0.4),
+        "Right Posterior Arcuate": (0.5, 0.95, 0.7),
         "Left Vertical Occipital": vof_l_base,
         "Right Vertical Occipital": vof_r_base,
         "Left V1V3": vof_l_shades[0],
@@ -141,6 +141,10 @@ COLOR_DICT = OrderedDict(
         "Callosum Posterior Parietal": (0.8, 0.4, 0.47),
         "Callosum Occipital": (0.67, 0.27, 0.6),
         "Callosum Temporal": (0.53, 0.13, 0.33),
+        "Left Optic Radiation": (0.0, 0.15, 0.75),
+        "Right Optic Radiation": (0.3, 0.4, 0.95),
+        "Left Temporo-parietal": (0.65, 0.0, 0.45),
+        "Right Temporo-parietal": (0.85, 0.4, 0.70),
     }
 )
 

{pyafq-3.1 → pyafq-3.2}/CHANGES.rst

@@ -1,3 +1,14 @@
+3.2 (May 26, 2026)
+==================
+Adds the temporo-parietal as a separate bundle from the
+posterior arcuate fasciculus. Updates default colors
+for some visual bundles for clarity. Adds mean signal DKI
+params as default tissue properties and switches DKI to DTI for default
+tissue properties.
+  * [FIX] More reliable brain masking/FA (#193)
+  * [ENH] Divide pARC (#194)
+  * [ENH] Change some visual bundle colors for pyAFQ (#192)
+
 3.1 (May 18, 2026)
 ==================
 Fixes a bug in VOF recogntion where some very far anterior

{pyafq-3.1 → pyafq-3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyAFQ
-Version: 3.1
+Version: 3.2
 Summary: pyAFQ: Automated Fiber Quantification ... in Python
 Home-page: https://tractometry.github.io/pyAFQ
 Download-URL: https://github.com/tractometry/pyAFQ

{pyafq-3.1 → pyafq-3.2}/docs/source/_static/custom.css

@@ -102,6 +102,14 @@ header.bd-header .navbar-brand > picture > img {
 .color-lightred { color: #ff9896; }
 .color-gold { color: #f2d94e; }
 .color-lightgold { color: #faeaa5; }
+.color-neonyellow { color: #f2d940; }
+.color-lightneonyellow { color: #faeb80; }
+.color-neonblue { color: #0026bf; }
+.color-lightneonblue { color: #4d66f2; }
+.color-neonmagenta { color: #a60073; }
+.color-lightneonmagenta { color: #d966b3; }
+.color-posteriorarcuate { color: #00b266; }
+.color-lightposteriorarcuate { color: #7ff2b3; }
 
 /* Callosum Colors */
 .color-darkgreen { color: #124730; }

{pyafq-3.1 → pyafq-3.2}/docs/source/reference/fibertracts.rst

@@ -60,6 +60,30 @@ Major Fiber Tracts
 .. role:: lightgold
    :class: color-lightgold
 
+.. role:: neonyellow
+   :class: color-neonyellow
+
+.. role:: lightneonyellow
+   :class: color-lightneonyellow
+
+.. role:: neonblue
+   :class: color-neonblue
+
+.. role:: lightneonblue
+   :class: color-lightneonblue
+
+.. role:: neonmagenta
+   :class: color-neonmagenta
+
+.. role:: lightneonmagenta
+   :class: color-lightneonmagenta
+
+.. role:: posteriorarcuate
+   :class: color-posteriorarcuate
+
+.. role:: lightposteriorarcuate
+   :class: color-lightposteriorarcuate
+
 .. role:: darkgreen
    :class: color-darkgreen
 
@@ -145,12 +169,12 @@ Major Fiber Tracts
      - 
      - 
    * - Left Superior Longitudinal
-     - :grey:`Grey`
+     - :neonyellow:`Neon Yellow`
      - 
      - 
      - 
    * - Right Superior Longitudinal
-     - :lightgrey:`Light Grey`
+     - :lightneonyellow:`Light Neon Yellow`
      - 
      - 
      - 
@@ -175,12 +199,12 @@ Major Fiber Tracts
      - 
      - 
    * - Left Posterior Arcuate
-     - :red:`Red`
+     - :posteriorarcuate:`Green`
      - 
      - 
      - 
    * - Right Posterior Arcuate
-     - :lightred:`Light Red`
+     - :lightposteriorarcuate:`Light Green`
      - 
      - 
      - 
@@ -275,12 +299,22 @@ Major Fiber Tracts
      - 
      - 
    * - Left Optic Radiation
-     - 
+     - :neonblue:`Neon Blue`
      - :cite:`Caffarra2021`
      - Optic Radiations
      - `Optic Radiations Example <../howto/howto_examples/optic_radiations.html>`_
    * - Right Optic Radiation
+     - :lightneonblue:`Light Neon Blue`
+     - 
+     - 
+     - 
+   * - Left Temporo-parietal
+     - :neonmagenta:`Neon Magenta`
+     - 
+     - 
      - 
+   * - Right Temporo-parietal
+     - :lightneonmagenta:`Light Neon Magenta`
      - 
      - 
      - 

{pyafq-3.1 → pyafq-3.2}/docs/source/reference/kwargs.rst

@@ -30,7 +30,7 @@ onnx_inter_threads: int
 	The number of inter threads to use for onnx models. Increasing will increase memory usage significantly. Default: 1
 
 brain_mask_definition: instance from `AFQ.definitions.image`
-	This will be used to create the brain mask, which gets applied before registration to a template. If you want no brain mask to be applied, use FullImage. If None, use Brainchop Mindgrab model. Default: None
+	This will be used to create the brain mask, which gets applied before registration to a template. If you want no brain mask to be applied, use FullImage. If None, use Synthseg model. Default: None
 
 
 ==========================================================
@@ -136,7 +136,7 @@ n_points_profile: int
 	Number of points to resample each streamline to before calculating the tract-profiles. Default: 100
 
 scalars: list of strings and/or scalar definitions
-	List of scalars to use. Can be any of: "dti_fa", "dti_md", "dki_fa", "dki_md", "dki_awf", "dki_mk", or other scalars found in AFQ.tasks.data. Can also be a scalar from AFQ.definitions.image. Finally, can also be "t1w". Defaults for single shell data to ["dti_fa", "dti_md", "t1w"], and for multi-shell data to ["dki_fa", "dki_md", "dki_kfa", "dki_mk", "t1w"]. Default: ['dti_fa', 'dti_md', 't1w']
+	List of scalars to use. Can be any of: "dti_fa", "dti_md", "dki_fa", "dki_md", "dki_awf", "dki_mk", or other scalars found in AFQ.tasks.data. Can also be a scalar from AFQ.definitions.image. Finally, can also be "t1w". Defaults for single shell data to ["dti_fa", "dti_md", "t1w_over_b0"], and for multi-shell data to ["dti_fa", "dti_md", "t1w_over_b0", "msdki_msd", "msdki_msk"]. Default: ['dti_fa', 'dti_md', 't1w_over_b0']
 
 
 ==========================================================

{pyafq-3.1 → pyafq-3.2}/examples/howto_examples/cloudknot_example.py

@@ -66,8 +66,7 @@ def afq_process_subject(subject):
     myafq = GroupAFQ(
         "local_bids_dir",
         dwi_preproc_pipeline="pipeline_name",
-        viz_backend_spec='plotly',  # this will generate both interactive html and GIFs # noqa
-        scalars=["dki_fa", "dki_md"])
+        viz_backend_spec='plotly')  # this will generate both interactive html and GIFs # noqa
 
     # export_all runs the entire pipeline and creates many useful derivates
     myafq.export_all()

{pyafq-3.1 → pyafq-3.2}/examples/tutorial_examples/plot_001_group_afq_api.py

@@ -128,13 +128,13 @@ myafq = GroupAFQ(
     tracking_params=tracking_params)
 
 ##########################################################################
-# Calculating DKI FA (Diffusion Kurtosis Imaging Fractional Anisotropy)
+# Calculating DTI FA (Diffusion Tensor Imaging Fractional Anisotropy)
 # ------------------------------------------------------------------
 # The GroupAFQ object has a method called `export`, which allows the user
 # to calculate various derived quantities from the data.
 #
-# For example, FA can be computed using the DKI model, by explicitly
-# calling `myafq.export("dki_fa")`. This triggers the computation of DKI
+# For example, FA can be computed using the DTI model, by explicitly
+# calling `myafq.export("dti_fa")`. This triggers the computation of DTI
 # parameters for all subjects in the dataset, and stores the results in
 # the AFQ derivatives directory. In addition, it calculates the FA
 # from these parameters and stores it in a different file in the same
@@ -142,7 +142,7 @@ myafq = GroupAFQ(
 #
 # .. note::
 #
-#    The AFQ API computes quantities lazily. This means that DKI parameters
+#    The AFQ API computes quantities lazily. This means that DTI parameters
 #    are not computed until they are required. This means that the first
 #    line below is the one that requires time.
 #
@@ -151,7 +151,7 @@ myafq = GroupAFQ(
 # This means that to extract the filename corresponding to the FA of the first
 # subject, we can do:
 
-FA_fname = myafq.export("dki_fa", collapse=False)["NDARAA948VFH"]["HBNsiteRU"]
+FA_fname = myafq.export("dti_fa", collapse=False)["NDARAA948VFH"]["HBNsiteRU"]
 
 # We will then use `nibabel` to load the deriviative file and retrieve the
 # data array.
@@ -240,7 +240,12 @@ fig_files = myafq.export("tract_profile_plots", collapse=False)[
 profiles_df = myafq.combine_profiles()
 altair_df = ava.combined_profiles_df_to_altair_df(
     profiles_df,
-    tissue_properties=['dki_fa', 'dki_md'])
+    tissue_properties=[
+        "dti_fa",
+        "dti_md",
+        "t1w_over_b0",
+        "msdki_msd",
+        "msdki_msk"])
 altair_chart = ava.altair_df_to_chart(altair_df)
 altair_chart.display()
 

{pyafq-3.1 → pyafq-3.2}/examples/tutorial_examples/plot_002_participant_afq_api.py

@@ -145,27 +145,27 @@ myafq = ParticipantAFQ(
 )
 
 ##########################################################################
-# Calculating DKI FA (Diffusion Tensor Imaging Fractional Anisotropy)
+# Calculating DTI FA (Diffusion Tensor Imaging Fractional Anisotropy)
 # ------------------------------------------------------------------
 # The ParticipantAFQ object has a method called ``export``, which allows the user
 # to calculate various derived quantities from the data.
 #
-# For example, FA can be computed using the DKI model, by explicitly
-# calling ``myafq.export("dki_fa")``. This triggers the computation of DKI
+# For example, FA can be computed using the DTI model, by explicitly
+# calling ``myafq.export("dti_fa")``. This triggers the computation of DTI
 # parameters, and stores the results in the AFQ derivatives directory.
 # In addition, it calculates the FA from these parameters and stores it in a
 # different file in the same directory.
 #
 # .. note::
 #
-#    The AFQ API computes quantities lazily. This means that DKI parameters
+#    The AFQ API computes quantities lazily. This means that DTI parameters
 #    are not computed until they are required. This means that the first
 #    line below is the one that requires time.
 #
 # The result of the call to ``export`` is the filename of the corresponding FA
 # files.
 
-FA_fname = myafq.export("dki_fa")
+FA_fname = myafq.export("dti_fa")
 
 ##########################################################################
 # We will then use ``nibabel`` to load the deriviative file and retrieve the

{pyafq-3.1 → pyafq-3.2}/examples/tutorial_examples/plot_004_export.py

@@ -100,24 +100,24 @@ myafq.export("help")
 
 
 ##########################################################################
-# Calculating DKI FA (Diffusion Tensor Imaging Fractional Anisotropy)
+# Calculating DTI FA (Diffusion Tensor Imaging Fractional Anisotropy)
 # ------------------------------------------------------------------
-# FA can be computed using the DKI model, by explicitly calling
-# ``myafq.export("dki_fa")``. This triggers the computation of DKI parameters,
+# FA can be computed using the DTI model, by explicitly calling
+# ``myafq.export("dti_fa")``. This triggers the computation of DTI parameters,
 # and stores the results in the AFQ derivatives directory. In addition, it
 # calculates the FA from these parameters and stores it in a different file in
 # the same directory.
 #
 # .. note::
 #
-#    The AFQ API computes quantities lazily. This means that DKI parameters
+#    The AFQ API computes quantities lazily. This means that DTI parameters
 #    are not computed until they are required. This means that the first
 #    line below is the one that requires time.
 #
 # The result of the call to ``export`` is the filename of the corresponding FA
 # files.
 
-FA_fname = myafq.export("dki_fa")
+FA_fname = myafq.export("dti_fa")
 
 
 ##########################################################################

{pyafq-3.1 → pyafq-3.2}/pyAFQ.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyAFQ
-Version: 3.1
+Version: 3.2
 Summary: pyAFQ: Automated Fiber Quantification ... in Python
 Home-page: https://tractometry.github.io/pyAFQ
 Download-URL: https://github.com/tractometry/pyAFQ