# Changing window/level and index slice for a volume loaded from the command line

**URL:** <https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924>\
**Category:** Support\
**Created:** [August 7, 2019, 5:24pm UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924 "2019-08-07T17:24:27Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![matt-warkentin](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/matt-warkentin/32/4962_2.png) [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Post date:** [August 7, 2019, 5:24pm UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/1 "2019-08-07T17:24:27Z")

</div>

Hi,

I am trying to write a piece of code that will open the Slicer GUI from the command-line, and load a particular volume, with a chosen window/level, and some fiducials pre-loaded into the scene. The code below partially works, in that it loads the volume and fiducials, but I can’t get the window/level change to work.

```auto
/Applications/Slicer\ 2.app/Contents/MacOS/Slicer \
--python-code "volumeNode = slicer.util.loadVolume('200056.nrrd', returnNode=True); displayNode = volumeNode.GetDisplayNode(); displayNode.AutoWindowLevelOff(); displayNode.SetWindow(1400); displayNode.SetLevel(-500)" \
--point F.fcsv

```

Any idea what I need to change to get things working?

Also, I would eventually like to extend this code to also open the volume (DICOM series) to a specific index slice. I found the following code at this [link](https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Launching_Slicer):

```auto
layoutManager = slicer.app.layoutManager()
red = layoutManager.sliceWidget('Red')
redLogic = red.sliceLogic()
# Print current slice offset position
print(redLogic.GetSliceOffset())
# Change slice position
redLogic.SetSliceOffset(20)

```

Is this the correct code to modify to specify a slice for the Slicer GUI to open at?

---

<div class="post-metadata">

**Author:** ![matt-warkentin](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/matt-warkentin/32/4962_2.png) [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Post date:** [August 7, 2019, 11:20pm UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/2 "2019-08-07T23:20:35Z")

</div>

I ended up figuring things out, here is what I did, in case it is of use for others…

Basically I was not “getting” the node correctly. Once I did, things worked properly. The code below will open the NRRD volume (200056.nrrd), change to lung windows (1400, -500), navigate to the index slice based on physical space, and add the fiducials.

To convert from slice number to physical space (offset), I took the RAS origin for inferior/superior axis which was -303.15, and “added” the distance to the index slice (index slice number (108) multiplied by the slice thickness (2.0 mm)). The fiducial file was previously saved from a Slicer session whereby I added two fiducials to arbitrary locations for testing purposes.

```auto
/Applications/Slicer\ 2.app/Contents/MacOS/Slicer --python-code "volumeNode = slicer.util.loadVolume('200056.nrrd', returnNode=True); volumeNode = getNode('200056'); displayNode = volumeNode.GetDisplayNode(); displayNode.AutoWindowLevelOff(); displayNode.SetWindow(1400); displayNode.SetLevel(-500); layoutManager = slicer.app.layoutManager(); red = layoutManager.sliceWidget('Red'); redLogic = red.sliceLogic(); redLogic.SetSliceOffset(-87.150)" --pointfile F.fcsv

```

The above code was ran in a bash shell on Mac OS.

---

<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:** [August 8, 2019, 1:13am UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/3 "2019-08-08T01:13:14Z")

</div>

You can jump all slice views to a specific physical location using this code snippet:

```
slicer.modules.markups.logic().JumpSlicesToLocation(mean_Ras[0], mean_Ras[1], mean_Ras[2], True)

```

See complete example here: [https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get\_centroid\_of\_a\_segment\_in\_world\_.28RAS.29\_coordinates](https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_centroid_of_a_segment_in_world_.28RAS.29_coordinates)

See examples of conversion between volume voxel and physical coordinates here: [https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get\_markup\_fiducial\_RAS\_coordinates\_from\_volume\_voxel\_coordinates](https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_markup_fiducial_RAS_coordinates_from_volume_voxel_coordinates)

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<div class="post-metadata">

**Author:** ![matt-warkentin](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/matt-warkentin/32/4962_2.png) [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Post date:** [August 10, 2019, 1:28am UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/4 "2019-08-10T01:28:36Z")

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Thanks for the response, @lassoan. Is it also possible to open a CT axial view (red) to a location based on the slice number/index, rather than the physical location? For example, open the CT to slice 108, rather than -85.150mm.

Something like this code:

```auto
redLogic.SetSliceOffset(-87.150)

```

But for slice number, rather than offset from the origin.

---

<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:** [August 10, 2019, 4:33am UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/5 "2019-08-10T04:33:17Z")

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For most images that are read from DICOM, slices are stacked along the third (K) axis, so “slice number” (more accurately, _InstanceNumber (0020,0013)_) is often (K + 1) but it can be also (number of slices - K) or something else, because when DICOM readers reconstruct a volume, they don’t keep track of slice numbers and they may flip and interpolate slices (if they are not equally spaced) as needed.

If you need a robust mechanism to find closest slice index corresponding to a position, then you need to read _ImagePositionPatient_ and _ImageOrientationPatient_ tags for all the slices of the image, find the closest slice, and then get _InstanceNumber_ of that slice.

Show DICOM slice number comes up time-to-time as a feature request, so if you implement this mechanism then it would be great if you could contribute it.

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 10, 2019, 4:58pm UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924/6 "2019-08-10T16:58:00Z")

</div>

Also, FYI, if you load your images via the DICOM module as scalar volumes the `DICOM.instanceUIDs` attribute of the MRML node will have a list of `SOPInstanceUID`s in slice order (the `k` dimension of IJK) so you can use that to look up the `InstanceNumber`.

[Here’s some code](https://github.com/Slicer/Slicer/blob/2b25e080bce23609710ad87a82030d3fe01c4286/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py#L572) that uses the dicom information for display (this could be extended to show the instance number in the case where the slice orientation corresponds to the acquisition plane)