try this

yeatmanlab · Jan 19, 2024 · d2f05b2 · d2f05b2
1 parent 9190ca7
commit d2f05b2
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Showing 2 changed files with 40 additions and 12 deletions.
diff --git a/AFQ/tasks/tractography.py b/AFQ/tasks/tractography.py
@@ -224,6 +224,7 @@ def gpu_tractography(data_imap, tracking_params, seed, stop,
     sft = gpu_track(
         data_imap["data"], data_imap["gtab"],
         nib.load(seed), nib.load(stop),
+        tracking_params["odf_model"],
         tracking_params["seed_threshold"],
         tracking_params["stop_threshold"],
         tracking_params["thresholds_as_percentages"],

diff --git a/AFQ/tractography/gputractography.py b/AFQ/tractography/gputractography.py
@@ -5,7 +5,7 @@
 from tqdm import tqdm
 
 from dipy.data import small_sphere
-from dipy.reconst.shm import CsaOdfModel
+from dipy.reconst.shm import OpdtModel, CsaOdfModel
 from dipy.reconst import shm
 from dipy.tracking import utils
 from dipy.io.stateful_tractogram import StatefulTractogram, Space
@@ -16,7 +16,7 @@
 
 
 # Modified from https://github.com/dipy/GPUStreamlines/blob/master/run_dipy_gpu.py
-def gpu_track(data, gtab, seed_img, stop_img,
+def gpu_track(data, gtab, seed_img, stop_img, odf_model,
               seed_threshold, stop_threshold, thresholds_as_percentages,
               max_angle, step_size, sampling_density, ngpus):
     """
@@ -34,6 +34,8 @@ def gpu_track(data, gtab, seed_img, stop_img,
     stop_img : Nifti1Image
         A float or binary mask that determines a stopping criterion
         (e.g. FA).
+    odf_model : str, optional
+        One of {"OPDT", "CSA"}
     seed_threshold : float
         The value of the seed_img above which tracking is seeded.
     stop_threshold : float
@@ -62,8 +64,6 @@ def gpu_track(data, gtab, seed_img, stop_img,
     seed_data = seed_img.get_fdata()
     stop_data = stop_img.get_fdata()
 
-    data = np.ascontiguousarray(data, dtype=np.float64)
-
     if len(np.unique(seed_data)) > 2:
         if thresholds_as_percentages:
             seed_threshold = get_percentile_threshold(
@@ -74,12 +74,25 @@ def gpu_track(data, gtab, seed_img, stop_img,
         stop_threshold = get_percentile_threshold(
             stop_data, stop_threshold)
 
-    model = CsaOdfModel(
-        gtab, sh_order=sh_order,
-        smooth=0.006, min_signal=1)
-    fit_matrix = model._fit_matrix
-    delta_b = fit_matrix
-    delta_q = fit_matrix
+    if odf_model.lower() == "opdt":
+        model = OpdtModel(
+            gtab,
+            sh_order=sh_order,
+            smooth=0.006,
+            min_signal=1)
+        fit_matrix = model._fit_matrix
+        delta_b, delta_q = fit_matrix
+    elif odf_model.lower() == "csa":
+        model = CsaOdfModel(
+            gtab, sh_order=sh_order,
+            smooth=0.006, min_signal=1)
+        fit_matrix = model._fit_matrix
+        delta_b = fit_matrix
+        delta_q = fit_matrix
+    else:
+        raise ValueError((
+            f"odf_model must be 'opdt' or "
+            "'csa', not {odf_model}"))
 
     sphere = small_sphere
     theta = sphere.theta
@@ -94,6 +107,20 @@ def gpu_track(data, gtab, seed_img, stop_img,
     H = shm.hat(B)
     R = shm.lcr_matrix(H)
 
+    data = np.ascontiguousarray(data, dtype=np.float64)
+    H = np.ascontiguousarray(H, dtype=np.float64)
+    R = np.ascontiguousarray(R, dtype=np.float64)
+    delta_b = np.ascontiguousarray(delta_b, dtype=np.float64)
+    delta_q = np.ascontiguousarray(delta_q, dtype=np.float64)
+    b0s_mask = np.ascontiguousarray(b0s_mask, dtype=np.int32)
+    stop_data = np.ascontiguousarray(stop_data, dtype=np.float64)
+    sampling_matrix = np.ascontiguousarray(
+        sampling_matrix, dtype=np.float64)
+    sph_verticies = np.ascontiguousarray(
+        sphere.vertices, dtype=np.float64)
+    sph_edges = np.ascontiguousarray(
+        sphere.edges, dtype=np.int32)
+
     gpu_tracker = cuslines.GPUTracker(
         cuslines.ModelType.CSAODF,
         radians(max_angle),
@@ -103,9 +130,9 @@ def gpu_track(data, gtab, seed_img, stop_img,
         0.25,  # relative peak threshold
         radians(45),  # min separation angle
         data, H, R, delta_b, delta_q,
-        b0s_mask.astype(np.int32), stop_data.astype(np.float64),
+        b0s_mask, stop_data,
         sampling_matrix,
-        sphere.vertices, sphere.edges.astype(np.int32),
+        sph_verticies, sph_edges,
         ngpus=ngpus, rng_seed=0)
 
     seed_mask = utils.seeds_from_mask(