pyAFQ 3.1__tar.gz → 3.3__tar.gz

{pyafq-3.1 → pyafq-3.3}/.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
 skip = [setup.cfg] 
-ignore-words-list = Reson, DNE, ACI, FPT, sagital, saggital, abd, Joo, Mapp, Commun, vor, Claus, coo
+ignore-words-list = Reson, DNE, ACI, FPT, sagital, saggital, abd, Joo, Mapp, Commun, vor, Claus, coo, ans

{pyafq-3.1 → pyafq-3.3}/.gitignore

@@ -5,8 +5,6 @@ AFQ/version.py
 docs/_build
 docs/build
 docs/source/auto_examples/
-docs/source/tutorials/tutorial_examples/
-docs/source/howto/howto_examples/
 docs/source/reference/config.rst
 examples/**/*.nii.gz
 examples/**/*.trk

{pyafq-3.1 → pyafq-3.3}/AFQ/_fixes.py

@@ -3,6 +3,7 @@ import math
 import tempfile
 from math import radians
 
+import imageio
 import numpy as np
 from dipy.align import vector_fields as vfu
 from dipy.align.imwarp import DiffeomorphicMap, mult_aff
@@ -11,7 +12,7 @@ from dipy.tracking.streamline import set_number_of_points
 from PIL import Image
 from scipy.linalg import blas, pinvh
 from scipy.special import gammaln, lpmv
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 logger = logging.getLogger("AFQ")
 
@@ -361,9 +362,9 @@ def gaussian_weights(
         return w
 
 
-def make_gif(show_m, out_path, n_frames=36, az_ang=-10, duration=150):
+def make_mp4(show_m, out_path, n_frames=720, az_ang=-0.5, fps=30, crf=35, verbose=True):
     """
-    Make a video from a Fury Show Manager.
+    Make an MP4 video from a Fury Show Manager with auto-cropping.
 
     Parameters
     ----------
@@ -371,28 +372,43 @@ def make_gif(show_m, out_path, n_frames=36, az_ang=-10, duration=150):
         The Fury Show Manager to use for rendering.
 
     out_path : str
-        The name of the output file.
+        The name of the output file
 
     n_frames : int
         The number of frames to render.
-        Default: 36
+        Default: 720
 
     az_ang : float
         The angle to rotate the camera around the
         z-axis for each frame, in degrees.
-        Default: -10
+        Default: -0.5
 
-    duration : int
-        The duration of each frame in the output GIF, in milliseconds.
-        Default: 150
+    fps : float
+        The frames per second for the output video.
+        Default: 30
+
+    crf : int
+        The Constant Rate Factor for the output video, which controls the
+        quality and file size. Lower values result in
+        higher quality and larger file sizes.
+        Default: 35 (very low quality, small file size)
+
+    verbose : bool
+        Whether to show a progress bar while generating the video.
+        Default: True
     """
+    if not out_path.lower().endswith(".mp4"):
+        out_path += ".mp4"
+
     video = []
 
     show_m.render()
     show_m.window.draw()
 
     with tempfile.TemporaryDirectory() as tmp_dir:
-        for ii in tqdm(range(n_frames), desc="Generating GIF", leave=False):
+        for ii in tqdm(
+            range(n_frames), desc="Generating MP4", leave=False, disable=not verbose
+        ):
             frame_fname = f"{tmp_dir}/{ii}.png"
             show_m.screens[0].controller.rotate((radians(az_ang), 0), None)
             show_m.render()
@@ -406,7 +422,6 @@ def make_gif(show_m, out_path, n_frames=36, az_ang=-10, duration=150):
         for img in video:
             arr = np.array(img)
             bg_color = arr[0, 0]
-
             mask = np.any(arr != bg_color, axis=-1)
 
             if np.any(mask):
@@ -421,20 +436,42 @@ def make_gif(show_m, out_path, n_frames=36, az_ang=-10, duration=150):
                 all_lower = max(all_lower, ymax)
 
         if all_left < all_right:
-            crop_box = (
-                max(0, all_left),
-                max(0, all_upper),
-                min(video[0].width, all_right),
-                min(video[0].height, all_lower),
-            )
+
+            def align_down(x, multiple=16):
+                return (x // multiple) * multiple
+
+            def align_up(x, multiple=16):
+                return ((x + multiple - 1) // multiple) * multiple
+
+            left = align_up(max(0, all_left), 16)
+            upper = align_up(max(0, all_upper), 16)
+            right = align_down(min(video[0].width, all_right), 16)
+            lower = align_down(min(video[0].height, all_lower), 16)
+
+            crop_box = (left, upper, right, lower)
             cropped_video = [img.crop(crop_box) for img in video]
         else:
             cropped_video = video
 
-        cropped_video[0].save(
+        width, height = cropped_video[0].size
+        with imageio.get_writer(
             out_path,
-            save_all=True,
-            append_images=cropped_video[1:],
-            duration=duration,
-            loop=1,
-        )
+            fps=fps,
+            format="ffmpeg",
+            codec="libx264",
+            pixelformat="yuv420p",
+            output_params=[
+                "-crf",
+                f"{str(int(crf))}",
+                "-preset",
+                "veryslow",
+                "-movflags",
+                "+faststart",
+            ],
+        ) as writer:
+            for img in cropped_video:
+                if img.size != (width, height):
+                    img = img.crop((0, 0, width, height))
+
+                frame_arr = np.array(img)
+                writer.append_data(frame_arr)

{pyafq-3.1 → pyafq-3.3}/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",
@@ -347,7 +387,7 @@ def default_bd():
                 "primary_axis": "I/S",
                 "ORG_spectral_subbundles": SpectralSubbundleDict(
                     {
-                        "Left V1V3": {
+                        "Left Early Visual": {
                             "cluster_IDs": [78],
                             "Left Optic Radiation": {
                                 "core": "Anterior",
@@ -409,7 +449,7 @@ def default_bd():
                 "primary_axis": "I/S",
                 "ORG_spectral_subbundles": SpectralSubbundleDict(
                     {
-                        "Right V1V3": {
+                        "Right Early Visual": {
                             "cluster_IDs": [78],
                             "Right Optic Radiation": {
                                 "core": "Anterior",

{pyafq-3.1 → pyafq-3.3}/AFQ/api/group.py

@@ -18,7 +18,7 @@ from dipy.io.stateful_tractogram import Space, StatefulTractogram
 from dipy.io.streamline import save_tractogram
 from dipy.utils.parallel import paramap
 from PIL import Image
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 import AFQ.api.bundle_dict as abd
 import AFQ.definitions.image as afm
@@ -555,7 +555,7 @@ class GroupAFQ(object):
                     ses
                 ]
                 seg_sft = aus.SegmentedSFT.fromfile(this_bundles_file, this_img)
-                seg_sft.sft.to_rasmm()
+                seg_sft.to_rasmm()
                 subses_info.append((seg_sft, this_mapping, this_img, this_reg_template))
 
             bundle_dict = self.export("bundle_dict", collapse=False)[
@@ -567,7 +567,7 @@ class GroupAFQ(object):
             for b in bundle_dict.bundle_names:
                 for i in range(len(self.valid_sub_list)):
                     seg_sft, mapping, img, reg_template = subses_info[i]
-                    idx = seg_sft.bundle_idxs[b]
+                    idx = seg_sft.get_bundle_idxs(b)
                     # use the first subses that works
                     # otherwise try each successive subses
                     if len(idx) == 0:

{pyafq-3.1 → pyafq-3.3}/AFQ/api/participant.py

@@ -8,7 +8,7 @@ from time import time
 import nibabel as nib
 from dipy.align import resample
 from PIL import Image, ImageDraw, ImageFont
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 import AFQ.utils.streamlines as aus
 from AFQ.api.utils import (

{pyafq-3.1 → pyafq-3.3}/AFQ/data/fetch.py

@@ -22,7 +22,7 @@ from dipy.io.streamline import (
 from dipy.segment.clustering import QuickBundles
 from dipy.segment.featurespeed import ResampleFeature
 from dipy.segment.metric import AveragePointwiseEuclideanMetric
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from AFQ._fixes import get_simplified_transform
 from AFQ.data.utils import aws_import_msg_error
@@ -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-3.3}/AFQ/models/asym_filtering.py

@@ -14,7 +14,7 @@ from dipy.data import get_sphere
 from dipy.direction import peak_directions
 from dipy.reconst.shm import sh_to_sf, sh_to_sf_matrix, sph_harm_ind_list
 from numba import config, njit, prange, set_num_threads
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 logger = logging.getLogger("AFQ")
 

{pyafq-3.1 → pyafq-3.3}/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-3.3}/AFQ/models/msmt.py

@@ -2,7 +2,7 @@ import numpy as np
 import osqp
 from dipy.reconst.mcsd import MSDeconvFit, MultiShellDeconvModel
 from scipy.sparse import csr_matrix
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 __all__ = ["MultiShellDeconvModel"]
 
@@ -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-3.3}/AFQ/nn/multiaxial.py

@@ -3,7 +3,7 @@ import os.path as op
 
 import nibabel as nib
 import numpy as np
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 from AFQ.data.fetch import afq_home, fetch_multiaxial_models
 from AFQ.nn.utils import prepare_t1_for_nn, resample_output

{pyafq-3.1 → pyafq-3.3}/AFQ/recognition/criteria.py

@@ -11,7 +11,7 @@ from dipy.segment.clustering import QuickBundles
 from dipy.segment.featurespeed import ResampleFeature
 from dipy.segment.metricspeed import AveragePointwiseEuclideanMetric
 from scipy.ndimage import distance_transform_edt
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from trx.io import load as load_trx
 
 import AFQ.recognition.cleaning as abc

{pyafq-3.1 → pyafq-3.3}/AFQ/recognition/utils.py

@@ -7,8 +7,9 @@ import dipy.tracking.streamlinespeed as dps
 import numpy as np
 from dipy.io.stateful_tractogram import Space, StatefulTractogram
 from dipy.io.streamline import save_tractogram
+from dipy.tracking import Streamlines
 from dipy.tracking.distances import bundles_distances_mdf
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
 axes_dict = {
     "L/R": 0,
@@ -125,11 +126,16 @@ def resample_tg(tg, n_points):
         if len(tg.shape) > 2:
             streamlines = tg.tolist()
             streamlines = [np.asarray(item) for item in streamlines]
+        else:
+            streamlines = [np.asarray(tg)]
     elif hasattr(tg, "streamlines"):
         streamlines = tg.streamlines
     else:
         streamlines = tg
 
+    streamlines = Streamlines(streamlines)
+    if streamlines._data.dtype != np.float32:
+        streamlines._data = streamlines._data.astype(np.float32)
     return dps.set_number_of_points(streamlines, n_points)
 
 

{pyafq-3.1 → pyafq-3.3}/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-3.3}/AFQ/tasks/segmentation.py

@@ -38,9 +38,7 @@ logger = logging.getLogger("AFQ")
 
 @immlib.calc("bundles")
 @as_file("_desc-bundles_tractography")
-def segment(
-    structural_imap, data_imap, mapping_imap, tractography_imap, segmentation_params
-):
+def segment(data_imap, mapping_imap, tractography_imap, segmentation_params):
     """
     full path to a trk/trx file containing containing
     segmented streamlines, labeled by bundle
@@ -93,16 +91,15 @@ def segment(
         **segmentation_params,
     )
 
-    seg_sft = aus.SegmentedSFT(bundles)
-
-    if len(seg_sft.sft) < 1:
+    if len(bundles) == 0:
         raise ValueError("Fatal: No bundles recognized.")
 
+    seg_sft = aus.SegmentedSFT(bundles)
+
     if is_trx:
-        seg_sft.sft.dtype_dict = {"positions": np.float32, "offsets": np.uint32}
+        seg_sft.sft.dtype_dict = {"positions": np.float16, "offsets": np.uint32}
         tgram = TrxFile.from_sft(seg_sft.sft)
         tgram.groups = seg_sft.bundle_idxs
-
     else:
         tgram = seg_sft.sft
 
@@ -154,8 +151,8 @@ def export_bundles(base_fname, output_dir, bundles, tracking_params):
             if len(bundle_sft) > 0:
                 logger.info(f"Saving {fname}")
                 if is_trx:
-                    seg_sft.sft.dtype_dict = {
-                        "positions": np.float32,
+                    bundle_sft.dtype_dict = {
+                        "positions": np.float16,
                         "offsets": np.uint32,
                     }
                     trxfile = TrxFile.from_sft(bundle_sft)
@@ -209,15 +206,9 @@ def export_bundle_lengths(bundles):
             len_data[f"{bundle} Median"] = 0
             len_data[f"{bundle} Min"] = 0
             len_data[f"{bundle} Max"] = 0
-    len_data["Total Recognized Median"] = np.median(
-        seg_sft.sft._tractogram._streamlines._lengths
-    )
-    len_data["Total Recognized Min"] = np.min(
-        seg_sft.sft._tractogram._streamlines._lengths
-    )
-    len_data["Total Recognized Max"] = np.max(
-        seg_sft.sft._tractogram._streamlines._lengths
-    )
+    len_data["Total Recognized Median"] = np.median(seg_sft.get_lengths())
+    len_data["Total Recognized Min"] = np.min(seg_sft.get_lengths())
+    len_data["Total Recognized Max"] = np.max(seg_sft.get_lengths())
 
     counts_df = pd.DataFrame(
         data=len_data,
@@ -297,7 +288,7 @@ def tract_profiles(
     reference = nib.load(scalar_dict[list(scalar_dict.keys())[0]])
     seg_sft = aus.SegmentedSFT.fromfile(bundles, reference=reference)
 
-    seg_sft.sft.to_rasmm()
+    seg_sft.to_rasmm()
     for bundle_name in seg_sft.bundle_names:
         this_sl = seg_sft.get_bundle(bundle_name).streamlines
         if len(this_sl) == 0:
@@ -398,14 +389,14 @@ 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-3.3}/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-3.3}/AFQ/tasks/tractography.py

@@ -88,7 +88,7 @@ def streamlines(
 
     if is_trx:
         start_time = time()
-        dtype_dict = {"positions": np.float32, "offsets": np.uint32}
+        dtype_dict = {"positions": np.float32, "offsets": np.uint64}
 
         lazyt = aft.track(
             fodf,