BF/twaks

tractometry · Dec 5, 2024 · 07d7f3e · 07d7f3e
1 parent e98128b
commit 07d7f3e
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/AFQ/tasks/tractography.py b/AFQ/tasks/tractography.py
@@ -291,7 +291,7 @@ def custom_tractography(import_tract=None):
 
 @pimms.calc("streamlines")
 @as_file('_tractography', include_track=True)
-def gpu_tractography(data_imap, tracking_params, seed, stop,
+def gpu_tractography(data_imap, fodf, tracking_params, seed, stop,
                      tractography_ngpus=0, chunk_size=100000):
     """
     full path to the complete, unsegmented tractography file
@@ -313,8 +313,7 @@ def gpu_tractography(data_imap, tracking_params, seed, stop,
     if tracking_params["directions"] == "boot":
         data = data_imap["data"]
     else:
-        data = nib.load(
-            data_imap[tracking_params["odf_model"].lower() + "_params"]).get_fdata()
+        data = fodf.get_fdata()
 
     sphere = tracking_params["sphere"]
     if sphere is None:
@@ -392,8 +391,9 @@ def get_tractography_plan(kwargs):
             default_tracking_params[k] = kwargs["tracking_params"][k]
 
     kwargs["tracking_params"] = default_tracking_params
-    kwargs["tracking_params"]["odf_model"] =\
-        kwargs["tracking_params"]["odf_model"].upper()
+    if isinstance(kwargs["tracking_params"]["odf_model"], str):
+        kwargs["tracking_params"]["odf_model"] =\
+            kwargs["tracking_params"]["odf_model"].upper()
     if kwargs["tracking_params"]["seed_mask"] is None:
         kwargs["tracking_params"]["seed_mask"] = ScalarImage(
             kwargs["best_scalar"])

diff --git a/AFQ/tractography/tractography.py b/AFQ/tractography/tractography.py
@@ -25,7 +25,7 @@ def track(params_file, directions="prob", max_angle=30., sphere=None,
           seed_mask=None, seed_threshold=0, thresholds_as_percentages=False,
           n_seeds=1, random_seeds=False, rng_seed=None, stop_mask=None,
           stop_threshold=0, step_size=0.5, minlen=50, maxlen=250,
-          odf_model="CSD", basis_type="descoteaux07", tracker="local", 
+          odf_model="CSD", basis_type="descoteaux07", tracker="local",
           trx=False):
     """
     Tractography
@@ -149,13 +149,15 @@ def track(params_file, directions="prob", max_angle=30., sphere=None,
     else:
         raise ValueError(f"Unrecognized direction '{directions}'.")
 
+    logger.debug(f"Using basis type: {basis_type}")
+
     if odf_model == "DTI" or odf_model == "DKI":
         evals = model_params[..., :3]
         evecs = model_params[..., 3:12].reshape(params_img.shape[:3] + (3, 3))
         odf = tensor_odf(evals, evecs, sphere)
         dg = dg.from_pmf(odf, max_angle=max_angle, sphere=sphere)
     else:
-        dg = dg.from_shcoeff(model_params, max_angle=max_angle, sphere=sphere, 
+        dg = dg.from_shcoeff(model_params, max_angle=max_angle, sphere=sphere,
                              basis_type=basis_type, legacy=False)
 
     if tracker == "local":