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Write image orientation to MRD file #148

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Write image orientation to MRD file #148

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73d15d8
write image orientation to mrd
h3lg3 Feb 3, 2026
797e8a9
use DImension instead of dict
h3lg3 Feb 5, 2026
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1 change: 1 addition & 0 deletions src/console/interfaces/acquisition_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.")
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32 changes: 29 additions & 3 deletions src/console/utilities/data/write_acquisition_to_mrd.py
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Expand Up @@ -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

Expand All @@ -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:
Expand All @@ -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
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