# Trouble viewing PET image (mha file) in SimpleITK

**URL:** https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507
**Category:** Beginner Questions
**Tags:** dicom, simpleitk, python
**Created:** [November 21, 2022, 8:20am UTC](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507 "2022-11-21T08:20:18Z")
**Posts on this page:** 3
**Page:** 1

<div class="post-metadata">

### Author: ![debapriya](https://discourse.itk.org/letter_avatar_proxy/v4/letter/d/bc79bd/32.png) [@debapriya](https://discourse.itk.org/u/debapriya)
#### Post date: [November 21, 2022, 8:20am UTC](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507/1 "2022-11-21T08:20:18Z")

</div>

Hello,  
I am using the following python code to view a PET and an MR image.

```auto
fixed_image = sitk.ReadImage("PET.mha", sitk.sitkFloat64)
moving_image = sitk.ReadImage("MR.mha", sitk.sitkFloat64)

point_acquisition_interface = gui.RegistrationPointDataAquisition(
     fixed_image, moving_image, fixed_window_level=(215, 50)
 )

```

In the resulting display, details of the PET image is lost.

 ![image](https://discourse.itk.org/uploads/default/original/2X/b/be736843c404444a68deef9274e07e7f715d961e.jpeg)

The original PET image looks as follows, when viewed by a different viewer.

 ![PET](https://discourse.itk.org/uploads/default/original/2X/f/fec25c0e065802b74e16ef69706d53b3f420066f.jpeg)

How can I improve display of the PET image in SimpleITK?

---

<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: [November 21, 2022, 2:01pm UTC](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507/2 "2022-11-21T14:01:39Z")

</div>

Hello @debapriya,

You are explicitly setting the PET display values via the parameter `fixed_window_level=(215, 50)`. You will need to change these settings to something that is appropriate for your data. First, try without explicitly setting the value, internally this defaults to using the whole intensity range (as done below). If this doesn’t work, you can try various settings changing the `windowMinimum`, `windowMaximum` values:

```auto
import SimpleITK as sitk

file_name = 
fixed_image = sitk.ReadImage(file_name)

# Modify the following two lines
windowMinimum = float(sitk.GetArrayViewFromImage(fixed_image).min()) 
windowMaximum = float(sitk.GetArrayViewFromImage(fixed_image).max())

fixed_window_level = (windowMaximum-windowMinimum, (windowMaximum+windowMinimum)/2)
sitk.Show(sitk.Cast(sitk.IntensityWindowing(fixed_image, windowMinimum, windowMaximum, outputMinimum=0, outputMaximum=255), sitk.sitkUInt8))

```

---

<div class="post-metadata">

### Author: ![debapriya](https://discourse.itk.org/letter_avatar_proxy/v4/letter/d/bc79bd/32.png) [@debapriya](https://discourse.itk.org/u/debapriya)
#### Post date: [November 23, 2022, 6:41am UTC](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507/3 "2022-11-23T06:41:16Z")

</div>

Thank you @zivy . It worked.