# Problem with the code snippet in “Get information from segmentation nrrd file header” of ScriptRepository

**URL:** <https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608>\
**Category:** Support\
**Created:** [July 18, 2020, 11:30am UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608 "2020-07-18T11:30:38Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![shahrokh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shahrokh/32/1499_2.png) [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Post date:** [July 18, 2020, 11:30am UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608/1 "2020-07-18T11:30:38Z")

</div>

Hello Dear Developers and Users

I save RT structure in nrrd format (seg.nrrd suffix). Then I run the code in [ScriptRepository](https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_information_from_segmentation_nrrd_file_header). I noticed that Layer and LabelValue keys do not exist in header dictionary.

In my case, also the shape of voxels array (the output of read\_segmentation\_info) is (14, 375, 252, 101) and uint8 type, but the shape of output\_voxels array (the output of extract\_segments) is (375, 252, 101) and float64 type.

Then I change this code as following:

```
import nrrd
input_filename = "/home/sn/Ms.Arjmandi/commands/RTSTRUCTStudy1.seg.nrrd"
output_filename = "/home/sn/Ms.Arjmandi/commands/RTSTRUCTStudy1New.seg.nrrd"
segment_list = [("skin",0),("Bladder",1),("Femour_L",2),("Femour_R",3),("Rectum",4),("CTV 1",5),("CTV 2",6),("CTV LN",7),("Penile bulb",8),("PTV 60",9),("PTV 46",10),("PTV 72",11),("Bowel bag",12),("PTV TOTAL",13)]
voxels, header = nrrd.read(input_filename)

def read_segmentation_info(input_filename):
    header = nrrd.read_header(input_filename)
    segmentation_info = {}
    segments = []
    segment_index = 0
    while True:
        prefix = "Segment{0}_".format(segment_index)
        if not prefix + "ID" in header.keys():
            break
        segment = {}
        segment["index"] = segment_index
        segment["color"] = [float(i) for i in header[prefix + "Color"].split(" ")] # Segment0_Color:=0.501961 0.682353 0.501961
        segment["colorAutoGenerated"] = int(header[prefix + "ColorAutoGenerated"]) != 0 # Segment0_ColorAutoGenerated:=1
        segment["extent"] = [int(i) for i in header[prefix + "Extent"].split(" ")] # Segment0_Extent:=68 203 53 211 24 118
        segment["id"] = header[prefix + "ID"] # Segment0_ID:=Segment_1
        segment["name"] = header[prefix + "Name"] # Segment0_Name:=Segment_1
        segment["nameAutoGenerated"] = int(header[prefix + "NameAutoGenerated"]) != 0 # Segment0_NameAutoGenerated:=1
        #segment["labelValue"] = int(header[prefix + "LabelValue"]) # Segment0_LabelValue:=1
        segment["labelValue"] = segment_index
        #segment["layer"] = int(header[prefix + "Layer"]) # Segment0_Layer:=0
        segment["layer"] = segment_index
        
        tags = {}
        tags_str = header[prefix + "Tags"].split("|")
        for tag_str in tags_str:
            tag_str = tag_str.strip()
            if not tag_str:
                continue
            key, value = tag_str.split(":", maxsplit=1)
            tags[key] = value
        segment["tags"] = tags
        segments.append(segment)
        segment_index += 1
    segmentation_info["segments"] = segments
    return segmentation_info

segmentation_info = read_segmentation_info(input_filename)

def segment_from_name(segmentation_info, segment_name):
    for segment in segmentation_info["segments"]:
        if segment_name == segment["name"]:
            return segment
    raise KeyError('segment not found by name ' + segment_name)

def segment_names(segmentation_info):
    names = []
    for segment in segmentation_info["segments"]:
        names.append(segment["name"])
    return names

def extract_segments(voxels, header, segmentation_info, segment_list):
    import numpy as np
    import re
    # Create empty array from last 3 dimensions (output will be flattened to a 3D array)
    output_voxels = np.zeros(voxels.shape)
    # Copy non-segmentation fields to the extracted header
    output_header = {}
    for key in header.keys():
        if not re.match("^Segment[0-9]+_.+", key):
            output_header[key] = header[key]
    # Copy extracted segments
    #dims = len(voxels.shape)
    for output_segment_index, segment_name_to_label_value in enumerate(segment_list):
        # Copy relabeled voxel data
        segment = segment_from_name(segmentation_info, segment_name_to_label_value[0])
        #print("segment_name_to_label_value[0]: ", segment_name_to_label_value[0])
        input_label_value = segment["labelValue"]
        print("input_label_value = ", input_label_value)
        output_label_value = segment_name_to_label_value[1]
        print("output_label_value = ", output_label_value)
        inputLayer = segment["layer"]
        print("inputLayer = ", inputLayer)
        output_voxels[inputLayer,voxels[inputLayer,:,:,:] == input_label_value] = output_label_value
        print("output_voxels size", output_voxels.shape) 
        # Copy all segment fields corresponding to this segment
        for key in header.keys():
            prefix = "Segment{0}_".format(segment["index"])
            matched = re.match("^"+prefix+"(.+)", key)
            if matched:
                field_name = matched.groups()[0]
                if field_name == "labelValue":
                    value = output_label_value
                elif field_name == "layer":
                    # output is a single layer (3D volume)
                    value = 0
                else:
                    value = header[key]
                print("output_segment_index = ", output_segment_index)
                output_header["Segment{0}_".format(output_segment_index) + field_name] = value
    # Remove unnecessary 4th dimension (volume is collapsed into 3D)
    # Remove "none" from "none (0,1,0) (0,0,-1) (-1.2999954223632812,0,0)"
    output_header["space directions"] = output_header["space directions"][-3:,:]
    # Remove "list" from "list domain domain domain"
    output_header["kinds"] = output_header["kinds"][-3:]
    output_voxels = np.uint8(output_voxels)
    return output_voxels, output_header

output_voxels, output_header = extract_segments(voxels, header, segmentation_info, segment_list)
print("final voxels size = ", voxels.shape)
print("final output_voxels size = ", output_voxels.shape)
nrrd.write(output_filename, output_voxels, output_header)

```

After editing it, when I want to add data (RTSTRUCTStudy1New.seg.nrrd) into 3DSlicer, loading … is paused and get the following message:

![paused](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/a/cad0a7db3b39d9396595eed79aaea587a97c1763.png)

Please guide me.  
Best regards,  
Shahrokh

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 18, 2020, 3:01pm UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608/2 "2020-07-18T15:01:13Z")

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The exception indicates that you created an invalid file. If you compared the header that you created with a valid file’s header then you will see how to change your script.

The script assumes you process segmentation created by a recent Slicer-4.11 release. It also flattens the segmentation into a single layer, as this script is for creating segmentation for third-party software, and most software only support 3D segmentation files (not 4D).

---

<div class="post-metadata">

**Author:** ![shahrokh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shahrokh/32/1499_2.png) [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Post date:** [July 19, 2020, 7:09am UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608/3 "2020-07-19T07:09:32Z")

</div>

> [@shahrokh](#):
>
> Layer and LabelValue keys do not exist in header dictionary.

Dear Andras

Thanks a lot for your guidance. As mentioned you, I run in 3DSlicer version 4.11.0-2019-09-20. Unfortunately, I get same error.

Afterwards, I check the code snippet available in ScriptRepository, without any changes. As mentioned before, **Layer** and **LabelValue** keys do not exist in header dictionary.

![aaa](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/4/44ed2c589a831a78bcf148db8257c733df7cc033.png)

As seen above, these tow keys do not exist in header dictionary.  
I must mentioned that I convert RT Structure (DICOM file) from **seg.vtm** to **seg.nrrd** and then run the code in ScriptRepository.

Please guide me.  
Thanks a lot.  
Shahrokh.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 20, 2020, 2:09am UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608/4 "2020-07-20T02:09:10Z")

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> [@shahrokh](#):
>
> I run in 3DSlicer version 4.11.0-2019-09-20

As I mentioned, you need to use a recent Slicer Preview Release. By that I mean a few day or max few weeks old version.

---

<div class="post-metadata">

**Author:** ![shahrokh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shahrokh/32/1499_2.png) [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Post date:** [July 20, 2020, 12:46pm UTC](https://discourse.slicer.org/t/problem-with-the-code-snippet-in-get-information-from-segmentation-nrrd-file-header-of-scriptrepository/12608/5 "2020-07-20T12:46:27Z")

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> [@shahrokh](#):
>
> Dear Andras

Dear Andras

Thanks a lot for your guidance. I run commands in Slicer-4.11.0-2020-07-18 without any problems.  
Best regards.  
Shahrokh