add scenario1 as yaml.

paquiteau · Nov 24, 2023 · bda6d81 · bda6d81
1 parent 09bd6f2
commit bda6d81
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Showing 4 changed files with 12 additions and 8 deletions.
diff --git a/src/conf/reconstructors/zero_filled.yaml b/src/conf/reconstructors/zero_filled.yaml
@@ -1 +1 @@
-- adjoint: {}
+adjoint: {}
diff --git a/src/conf/experiments/scenario1.yaml → src/conf/scenario1.yaml b/src/conf/experiments/scenario1.yaml → src/conf/scenario1.yaml
@@ -1,7 +1,7 @@
-# @package _global
-#
 # This files contains the configuration to reproduce the scenario 1 of the Simfmri paper.
 
+force_sim: false
+
 simulation:
   sim_params:
     sim_tr: 0.1
@@ -14,7 +14,7 @@ simulation:
   handlers:
     phantom-brainweb:
       subject_id: 5
-      bbox: [0.225,-0.07, 0.06, -0.055, None, None]
+      bbox: [0.225,-0.07, 0.06, -0.055, null, null]
     activation-block:
       event_name: block_on
       block_on: 20
@@ -25,15 +25,18 @@ simulation:
       snr: 100
     acquisition-vds:
       shot_time_ms: 50
-      acs: 0.125
+      acs: 1
       accel: 1
-      accel_axis: 1
+      accel_axis: 0
       constant: true
       direction: top-down
+      smaps: false
 
 reconstructors:
   adjoint: {}
 
+stats:
+  contrast_name: block_on
 
 
 hydra:

diff --git a/src/simfmri/analysis/stats.py b/src/simfmri/analysis/stats.py
@@ -56,8 +56,8 @@ def contrast_zscore(
         drift_model=sim.extra_infos.get("drift_model", None),
     )
     # Create a mask from reference data (not ideal, but best)
-    mask = sim.data_ref[0] > 0
-    image_ = abs(image)[:, mask]
+    mask = sim.static_vol > 0
+    image_ = abs(image)[..., mask].squeeze()
     logger.debug(f"image_={image_.shape}, design matrix={design_matrix.shape}")
     labels, results = run_glm(image_, design_matrix.values)
     # Translate formulas to vectors

diff --git a/src/simfmri/cli/main.py b/src/simfmri/cli/main.py
@@ -41,6 +41,7 @@ def main_app(cfg: DictConfig) -> None:
             simulator, sim = HandlerChain.from_conf(cfg.simulation)
             sim = simulator(sim)
             del simulator
+            os.makedirs(cache_dir, exist_ok=True)
             with open(sim_file, "wb") as f:
                 pickle.dump(sim, f)