diff --git a/src/console/interfaces/acquisition_data.py b/src/console/interfaces/acquisition_data.py
index 1f6e6d99..1762bf51 100644
--- a/src/console/interfaces/acquisition_data.py
+++ b/src/console/interfaces/acquisition_data.py
@@ -210,6 +210,7 @@ def save_ismrmrd(
                 header=header,
                 sequence=self.sequence,
                 dataset_path=dataset_path,
+                channel_assignment=self.acquisition_parameters.channel_assignment,
             )
 
         log.warning("Invalid MRD header, could not write MRD file.")
diff --git a/src/console/utilities/data/write_acquisition_to_mrd.py b/src/console/utilities/data/write_acquisition_to_mrd.py
index 62125aa3..f10ea30f 100644
--- a/src/console/utilities/data/write_acquisition_to_mrd.py
+++ b/src/console/utilities/data/write_acquisition_to_mrd.py
@@ -6,6 +6,7 @@
 import numpy as np
 from pypulseq.Sequence.sequence import Sequence
 
+from console.interfaces.dimensions import Dimensions
 from console.interfaces.rx_data import RxData
 from console.utilities.data import get_logger, mrd_helper
 
@@ -17,6 +18,7 @@ def write_acquisition_to_mrd(
     header: ismrmrd.xsd.ismrmrdHeader,
     sequence: Sequence,
     dataset_path: Path,
+    channel_assignment: Dimensions,
 ) -> Path:
     """Write imaging data to ISMRMRD."""
     with ismrmrd.Dataset(dataset_path) as dataset:
@@ -25,9 +27,33 @@ def write_acquisition_to_mrd(
         # Create acquisition
         acq = ismrmrd.Acquisition()
         acq.version = int(version("ismrmrd")[0])
-        acq.read_dir[0] = 1.0
-        acq.phase_dir[1] = 1.0
-        acq.slice_dir[2] = 1.0
+
+        # Set raw data orientation directions in LPS coordinates, assuming patient is lying supine, head first.
+        # This information is shared for all acquisitions
+        # The assumption is that the console output channels to physical gradient orientations are as follows
+        # ch output1 -> gradient from front to back (Patient: I to S)
+        # ch output2 -> gradient from top to bottom (Patient: P to A)
+        # ch output3 -> gradient from left to right (Patient: R to L)
+        # For LPS coordinates the direction P to A needs to be inverted, i.e., read_dir = [0,-1,0]
+
+        # Map logical gradient axes to physical directions in LPS coordinates
+        direction_map = {
+            1: (2, 1.0),   # I to S -> [0, 0, 1]
+            2: (1, -1.0),  # P to A -> [0, -1, 0] (inverted for LPS)
+            3: (0, 1.0),   # R to L -> [1, 0, 0]
+        }
+
+        # Set readout direction
+        idx, val = direction_map[int(channel_assignment.x)]
+        acq.read_dir[idx] = val
+
+        # Set phase encoding direction
+        idx, val = direction_map[int(channel_assignment.y)]
+        acq.phase_dir[idx] = val
+
+        # Set slice direction
+        idx, val = direction_map[int(channel_assignment.z)]
+        acq.slice_dir[idx] = val
 
         trajectory_position = 0
         none_counter = 0