# Get anatomical metadata from dicom in Python

**URL:** https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307
**Category:** Uncategorized
**Created:** [July 29, 2021, 7:09pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307 "2021-07-29T19:09:08Z")
**Posts on this page:** 14
**Page:** 1

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [July 29, 2021, 7:09pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/1 "2021-07-29T19:09:08Z")

</div>

I have dicom images converted to nifti format. I need to find if the images are of `carotid` or `coronary` vessels from the metadata. I have searched and am convinced that these metadata are not available in `Nifti.header`.

Are there ways to find that in dicoms using any python package? I can get the metadata using some C++ tools but need to implement the same in python.

 ![image](https://discourse.itk.org/uploads/default/original/2X/b/bdd757e1a7b44c8b7c637aa563bb546687e614e4.png)

---

<div class="post-metadata">

### Author: ![zivy](https://discourse.itk.org/user_avatar/discourse.itk.org/zivy/32/1726_2.png) [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [July 29, 2021, 7:42pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/2 "2021-07-29T19:42:08Z")

</div>

Hello @banikr,

Indeed with nifti you loose all of the rich DICOM header information.

Using SimpleITK (\>=2.1.0) and your original DICOM image:

```auto
import SimpleITK as sitk
image = sitk.ReadImage('my_dicom_image.dcm')

# ignore leading/trailing whitespace and upper/lower case
if image['0018|0015'].strip().lower()== 'carotid':
  print('carotid')

```

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [July 29, 2021, 8:47pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/3 "2021-07-29T20:47:53Z")

</div>

Hi, I have got the following error with codes:

```auto
casePath = r'/media/banikr2/CAP_Exam_Data2/OrganizedFolder2/dicoms/im0-1.3.6.1.4.1.5962'
dcmItk = dicomread(casePath) #, imgitk=True)
print(dcmItk.GetSize())
if dcmItk['0018|0015'].strip().lower()== 'carotid':
  print('carotid')

```

```auto
(512, 512, 559)
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-19-372160a971c2> in <module>
      2 dcmItk = dicomread(casePath) #, imgitk=True)
      3 print(dcmItk.GetSize())
----> 4 if dcmItk['0018|0015'].strip().lower()== 'carotid':
      5 print('carotid')

~/miniconda3/envs/carotid36/lib/python3.6/site-packages/SimpleITK/SimpleITK.py in __getitem__ (self, idx)
   3724 
   3725 if (len(idx) > dim):
-> 3726 raise IndexError("too many indices for image")
   3727 
   3728 # All the indices are integers just return GetPixel value

IndexError: too many indices for image

```

Another question: are these values `0018|0015` indicate anatomical metadata for all the dicoms?

Additional info: the dicom files nor have `.dcm` extension neither in single file. Rather are in multiple series/slices.  
`dicomread` function encompasses the following codes to read the image given the case/folder path:

```auto
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(casePath)
reader.SetFileNames(dicom_names)
image = reader.Execute()

```

---

<div class="post-metadata">

### Author: ![zivy](https://discourse.itk.org/user_avatar/discourse.itk.org/zivy/32/1726_2.png) [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [July 30, 2021, 7:59pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/4 "2021-07-30T19:59:43Z")

</div>

Hello @banikr,

1. The file extension doesn’t matter as you called the reader’s `GetGDCMSeriesFileNames` which will try all files and return the files associated with the first DICOM series it encounters.
2. The tag, 0018|0015 corresponds to [BodyPartExamined](https://dicom.innolitics.com/ciods/raw-data/general-series/00180015), which is defined by the DICOM standard.
3. To see which DICOM tags were loaded: `image.GetMetaDataKeys()`.
4. You are likely using a SimpleITK version \<2.1.0, hence the error (see original response above which specifically says version \>=2.1.0). For older versions the syntax is `image.GetMetaData('0018|0015').strip().lower()`

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [July 30, 2021, 10:31pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/5 "2021-07-30T22:31:48Z")

</div>

> `>> SimpleITK. __version__ `  
> `'2.0.2'`

```auto
>> image = dicomread(dcmPath, True)
>> image.GetSize()
(512, 512, 240)

```

Now following the lower sitk version syntax:

```auto
image.GetMetaData('0018|0015').strip().lower()

```

This results in the following error:

```auto
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-35-d30ec7128239> in <module>
----> 1 image.GetMetaData('0018|0015').strip().lower()

~/miniconda3/envs/carotid36/lib/python3.6/site-packages/SimpleITK/SimpleITK.py in GetMetaData(self, key)
   3123 def GetMetaData(self, key):
   3124 r"""GetMetaData(Image self, std::string const & key) -> std::string"""
-> 3125 return _SimpleITK.Image_GetMetaData(self, key)
   3126 
   3127 def SetMetaData(self, key, value):

RuntimeError: Exception thrown in SimpleITK Image_GetMetaData: /tmp/SimpleITK-build/ITK/Modules/Core/Common/src/itkMetaDataDictionary.cxx:77:
itk::ERROR: Key '0018|0015' does not exist 

```

I think when reading dicom images by `sitk`, it doesn’t read and store all the metadata.  
Again, `image.GetMetaDataKeys()` results: `()`

The next thing I am gonna try is to install 2.1.0 version of sitk and check again.

---

<div class="post-metadata">

### Author: ![dchen](https://discourse.itk.org/user_avatar/discourse.itk.org/dchen/32/34_2.png) [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [July 31, 2021, 12:51am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/6 "2021-07-31T00:51:59Z")

</div>

Can you dump all the meta data keys that are in the image? This line ought to do it:

```
print(image.GetMetaDataKeys())

```

Or can you share an example image?

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [July 31, 2021, 12:57am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/7 "2021-07-31T00:57:37Z")

</div>

Hi, print also gives blank parenthesis.  
The data/.dcm is shared [here](https://drive.google.com/file/d/1b60AWAL3TqABX21_vnw9kfZNHHtRuawF/view?usp=sharing).

---

<div class="post-metadata">

### Author: ![dchen](https://discourse.itk.org/user_avatar/discourse.itk.org/dchen/32/34_2.png) [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [July 31, 2021, 1:08am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/8 "2021-07-31T01:08:14Z")

</div>

I’m not seeing the key ‘0008|0015’ in that image. Here’s the metadata dictionary that I see:

0008|0008 : ORIGINAL\PRIMARY\CARDIAC\_CTA  
0008|0016 : 1.2.840.10008.5.1.4.1.1.2.1  
0008|0018 : 1.3.6.1.4.1.19291.2.1.3.11689618230218138555609087104  
0008|0020 : 20130205  
0008|0021 : 20130205  
0008|0022 : 20130205  
0008|0023 : 20130205  
0008|002a : 20130205131533.872  
0008|0030 : 131102.000  
0008|0031 : 131453.077  
0008|0032 : 131529.230  
0008|0033 : 131533.872  
0008|0050 : CT5000089169  
0008|0060 : CT  
0008|0061 : CT  
0008|0070 : TOSHIBA  
0008|0080 : NIH Clinical Center  
0008|0090 : CHEN^MARCUS  
0008|1010 : 1C705A  
0008|1030 : CT Non-Cardiac Finding  
0008|103e : HALF 75% 0.97s Cardiac 0.5 CE  
0008|1040 : Radiology CT4  
0008|1090 : Aquilion ONE  
0008|2111 : LossLess compression with JPEG 2K, compression ratio 3.59  
0008|9205 : MONOCHROME  
0008|9206 : VOLUME  
0008|9207 : NONE  
0010|0010 : unnamed  
0010|0020 : PACI0061\_V1  
0010|0021 :  
0010|0030 : 19620130  
0010|0040 : F  
0010|1010 : 051Y  
0018|1000 : 1CB1262006  
0018|1020 : V4.93ER004  
0018|1030 : Cardiac Subtraction - Chen  
0018|1081 :  
0018|1082 :  
0018|1083 :  
0018|1084 :  
0018|5100 : FFS  
0018|9004 : PRODUCT  
0018|9037 : RETROSPECTIVE  
0018|9070 : 973  
0018|9073 : 4919  
0018|9085 : ECG  
0018|9169 : RR\_INTERVAL  
0020|000d : 1.3.6.1.4.1.19291.2.1.1.11689618230218138555609086992  
0020|000e : 1.3.6.1.4.1.19291.2.1.2.11689618230218138555609087103  
0020|0010 : 4000123328  
0020|0011 : 8  
0020|0012 : 6  
0020|0013 : 1  
0020|0020 : L\P  
0020|0052 : 1.2.392.200036.9116.2.5.1.37.2423320044.1360037467.302306  
0020|1040 :  
0020|1041 : 60.00  
0020|1208 : 1983  
0020|4000 : CTA\HALF  
0028|0002 : 1  
0028|0004 : MONOCHROME2  
0028|0008 : 240  
0028|0010 : 512  
0028|0011 : 512  
0028|0100 : 16  
0028|0101 : 16  
0028|0102 : 15  
0028|0103 : 1  
0028|2110 : 00  
0032|1060 : CT Non-Cardiac Finding  
0040|0002 : 20130205  
0040|0003 : 130207.000  
0040|0004 : 20130205  
0040|0005 : 133207.000  
0040|0007 : CT Non-Cardiac Finding  
0040|0009 : 5000089169  
0040|0244 : 20130205  
0040|0245 : 131102.000  
0040|0253 : 1022  
0040|1001 : 4000123328  
2050|0020 : IDENTITY  
ITK\_original\_direction : [UNKNOWN\_PRINT\_CHARACTERISTICS]

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [July 31, 2021, 1:35am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/9 "2021-07-31T01:35:54Z")

</div>

I see, then the metadata is not available inherently.  
Are there reasons for `image.GetMetaDataKeys()` not printing anything?  
How did you read the metadata? I am reading dicoms using `dicomread` shared in previous replies.

---

<div class="post-metadata">

### Author: ![dchen](https://discourse.itk.org/user_avatar/discourse.itk.org/dchen/32/34_2.png) [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [July 31, 2021, 1:46am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/10 "2021-07-31T01:46:45Z")

</div>

I’m not sure why your metadata dictionary is not printing anything. You can see the script I used here:

> <https://gist.github.com/dave3d/bf1f961a2628dd489ed09cbe9c0d6aae>

I ran it with the ‘-v’ flag.

---

<div class="post-metadata">

### Author: ![mihail.isakov](https://discourse.itk.org/letter_avatar_proxy/v4/letter/m/c4cdca/32.png) [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [July 31, 2021, 9:48am UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/11 "2021-07-31T09:48:58Z")

</div>

> [@](#):
>
> Here’s the metadata dictionary that I see

It is multi-frame IOD, only a very small part of DICOM attributes is visible, ‘metadata dictionary’ contains only top-level tags. In particular case there is related sequence is _shared groups_, but it is empty

 ![md](https://discourse.itk.org/uploads/default/original/2X/9/90fe5c0eb8dcac286e8f798d413b679d140fef35.jpeg)

**Edit:**  
P.S. BTW, anatomy description attributes are “Type 3”, optional.

**Edit:**  
There is also one close private tag, BTW

 ![pbp](https://discourse.itk.org/uploads/default/original/2X/6/68f87524e0accaf1afd8ff5b721f0d2bbb1736b2.jpeg)

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [August 4, 2021, 11:12pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/12 "2021-08-04T23:12:12Z")

</div>

I can read the metadata using the following `itk` functions for dicom or given a `casePath_`(name of the directory)

```auto
imageType = itk.Image[itk.F, 3]
# print(imageType)
reader = itk.ImageSeriesReader[imageType].New()
dicomIO = itk.GDCMImageIO.New() # GDCMImageIO is not available in sitk
dicomFN = itk.GDCMSeriesFileNames.New()
reader.SetImageIO(dicomIO)
dicomFN.SetUseSeriesDetails(True)
dicomFN.SetDirectory(casePath_)
uids = dicomFN.GetSeriesUIDs()
fnames = dicomFN.GetFileNames(uids[0])
reader.SetFileNames(fnames)
reader.Update()
# image = reader.GetOutput()
# ##------------------------------------------------------------------------------##
metaData = dicomIO.GetMetaDataDictionary()
# ## now you can access the meta data using indexing by key.
# ## The key we are conserned with is the body site key '0018|0015'
print(metaData['0018|0015'])

```

Are there any such versions in `sitk` to read the metadata?  
What I figured that `sitk` has no `GDCMImageIO` unlike `itk` and maybe `sitk` doesn’t support all the metadata readability as `itk`

---

<div class="post-metadata">

### Author: ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)
#### Post date: [August 4, 2021, 11:27pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/13 "2021-08-04T23:27:04Z")

</div>

Hello,  
`sitk.ReadImage` only works when the dicom files are saved in a single file with `.dcm` extension. But many dicom files are stored as multiple slices in a single directory. How do you suggest reading those dicoms’ metadata.

I use the following function to read both single `.dcm` and multiple sliced dicom images.

```auto
def dicomread(casePath, imgitk=None):
    if not os.path.isdir(casePath):
        print("The path doesn't exist.")
    reader = sitk.ImageSeriesReader()
    dicom_names = reader.GetGDCMSeriesFileNames(casePath)
    reader.SetFileNames(dicom_names)
    image = reader.Execute() # type --> 'SimpleITK.SimpleITK.Image'
    if image.GetDimension() == 4 and image.GetSize()[3] == 1:
# image = sitk.GetArrayFromImage(image)[0,...]
        image = image[:, :, :, 0]
    return image

```

would it be possible to add the metadata part you mentioned inside/with this function?

---

<div class="post-metadata">

### Author: ![zivy](https://discourse.itk.org/user_avatar/discourse.itk.org/zivy/32/1726_2.png) [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [August 5, 2021, 12:45pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307/14 "2021-08-05T12:45:52Z")

</div>

Hello @banikr,

The `reader` in your code contains all of the metadata. Please see [this usage example](https://simpleitk.readthedocs.io/en/master/link_DicomSeriesReadModifyWrite_docs.html) on read-the-docs, the relevant function is [GetMetaData](https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageSeriesReader.html#aa9ba914300ff9fe2e63241912cf98b8e).

Highly recommend that you spend some time skimming the SimpleITK documentation, specifically the [examples on read the docs](https://simpleitk.readthedocs.io/en/master/link_examples.html) and the [Jupyter notebooks](https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks) to better familiarize yourself with the toolkit.