Editing an Existing NRRD File

Hello! I have a quick question.

I’m using pynrrd to open an existing segmented NRRD file. I’m trying to remove certain segments that are there, then re-save without those removed segments.

I have many Segments, and each apparently is named SegmentX_Property, where “X” is their respective number (e.g., 1, 2, 3…) and “Property” is a property (e.g., Color, Name, etc.). I have a list of numbers (e.g., [1, 3, 5, 7]), representing segments I wish to keep.

Can someone help me in taking this list and my existing pynrrd file to output a new Segmented NRRD file with only Segments in my list of numbers?

Thank you so much in advanced!

I’ll include my code just for reference, though its scope extends beyond what I’m asking here.

import SimpleITK as sitk
import numpy as np
import nrrd

def filter_segments_by_name(nrrd_file_path, target_substrings):
        image = sitk.ReadImage(nrrd_file_path)
        filtered_names = []

        for key in image.GetMetaDataKeys():
            if key.endswith("_Name"):
                segment_name = image.GetMetaData(key)
                if any(substring.lower() in segment_name.lower() for substring in target_substrings):

        return filtered_names

    except Exception as e:
        print(f"Error reading NRRD file: {e}")
        return []

def filter_segments_properties(image, filtered_names):
    filtered_segments = []

    # Iterate over all metadata keys
    for key in image.GetMetaDataKeys():
        if key.startswith("Segment") and key.endswith("_Name"):
            segment_number = int(key.split("_")[0][len("Segment"):])
            segment_name = image.GetMetaData(key)
            if segment_name in filtered_names:

    return filtered_segments

def filter_segments(segments_to_keep, filename):
    Filters segments from an NRRD file based on the provided list of segment numbers.

        segments_to_keep (list[int]): List of segment numbers to retain.
        filename (str): Path to the input .seg.nrrd file.

        None. Saves the filtered data to a new NRRD file.
    # Load the .seg.nrrd file
    data, header = nrrd.read(filename)

    # Initialize an empty dictionary to store the filtered data
    filtered_data = {}

    # Iterate through each segment
    for segment_number in segments_to_keep:
        segment_key_prefix = f"Segment{segment_number}_"

        # Collect all keys associated with this segment
        segment_keys = [key for key in header.keys() if key.startswith(segment_key_prefix)]

        # Copy the segment data and its properties
        for key in segment_keys:
            filtered_data[key] = data[key]

    # Write the filtered data to a new NRRD file
    output_filename = 'filtered_segments.nrrd'
    nrrd.write(output_filename, filtered_data, header)

    print(f"Filtered data saved to {output_filename}")

# Load the NRRD file
**nrrd_file_path = [insert your .seg.nrrd file here]**
**save_path = [insert your path here for saving]**
data, header = nrrd.read(nrrd_file_path)
image = sitk.ReadImage(nrrd_file_path)

# Define your list of target substrings
target_substrings = ["rib", "vert"]

# Get the filtered segment names
filtered = filter_segments_by_name(nrrd_file_path, target_substrings)

# Filter the segments based on the names
segments_to_keep = filter_segments_properties(image, filtered)

# Create a set for efficient membership checking
segments_to_keep_set = set(segments_to_keep)

# Filter segments
for segment in list(header['labels']):
    if all(item in segments_to_keep_set for item in segment):
        # Segment contains all items from segments_to_keep
        # Remove this segment
        del header['labels'][segment]
        del header['sizes'][segment]
        del header['spacings'][segment]
        # Add any other relevant fields to remove

nrrd.write(save_path, data, header)

This is inplemented in slicerio Python package: you specify thr list of segment names and label values and you get a new nrrd file that only contains those segments, with the label values that you specified.


Thank you so much for your prompt reply. I have been trying to use this library, but cannot get a valid NRRD file to save at the end of the process with extracted features. See my code below:

import slicerio
import numpy as np
import nrrd

nrrd_file_path = [input file path]
save_path = [output file path]

# Load the existing NRRD file
nrrd_data, nrrd_header = nrrd.read(nrrd_file_path)

# Let's say I know I want to keep these three segments with these three corresponding Segment ID numbers (I assume that's what the numbers are for)
filtered_segment_names = ['L3 vertebra', 'L2 vertebra', 'L1 vertebra']  # Segment Names
filtered_numbers = [20, 21, 22]  # Segment IDs

# Construct segments_to_extract from these lists
segments_to_extract = {"Segment" + str(segment): label for segment, label in zip(filtered_segment_names, filtered_numbers)}

# Create a new NRRD data array filled with zeros
new_nrrd_data = np.zeros_like(nrrd_data)

# Loop over the segments and labels
for segment, label in segments_to_extract.items():
    # Find the indices where the segment is located in the original NRRD data
    indices = np.where(nrrd_data == segment)

    # Set these indices to the specified label value in the new NRRD data
    new_nrrd_data[indices] = label

# Write the new NRRD data to a new file using the existing header
nrrd.write(save_path, new_nrrd_data, nrrd_header)

See an example of how to do this using slicerio here.


Thank you kindly once again. I apologize for my rudimentary questions.
I now have a script that outputs a new .seg.nrrd file that has the correct segment names.

However, when I try actually using the file (say, in Stradview), an error occurs (see below).

Is it the segment_names_to_labels variable? For it, I input a paired list of segment names with their corresponding IDs. See code below error message for context.

# Imports
import slicerio
import nrrd

# Pre-defined Variables
nrrd_file_path = r"\Python Scripts\CTChest segmentation.seg.nrrd"
save_path = r"\Python Scripts\CTChest segmentation EDITED.seg.nrrd"
segment_names_to_labels = [('L3 vertebra', 20), ('L2 vertebra', 21), ('L1 vertebra', 22)]

# Load the existing NRRD file
voxels, header = nrrd.read(nrrd_file_path)

# Obtain NRRD segmentation information
segmentation_info = slicerio.read_segmentation_info(nrrd_file_path)

# Save new file with extracted data
extracted_voxels, extracted_header = slicerio.extract_segments(voxels, header, segmentation_info, segment_names_to_labels)
nrrd.write(save_path, extracted_voxels, extracted_header)