# Open lung CT tiff files

**URL:** <https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494>\
**Category:** Support\
**Tags:** segmentation, lungctanalyzer\
**Created:** [November 20, 2017, 5:54pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494 "2017-11-20T17:54:18Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![laura\_rodriguez](https://avatars.discourse-cdn.com/v4/letter/l/e495f1/32.png) [@laura\_rodriguez](https://discourse.slicer.org/u/laura_rodriguez)\
**Post date:** [November 20, 2017, 5:54pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/1 "2017-11-20T17:54:18Z")

</div>

Hello again

One silly question

I am trying to import tiff or bmp files to built a volume with 3dslicer, in theory it works, but, It only builds a multi-volume file, one for each slice. I would like it to build one single volume with all the slices, is it possible? Just in those cases in which I did not have dicom files. here I show you how I am trying to do it

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/0/b094cdf17ce63f6708ac23845790a931978ad2eb.png)

In volume menu this is what appears. I have to change parameters to built them in the correct size, but if I have to do this with each image it can be neverending.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/6/8639686b3f14afd154a8b0bde07ca17e438f0156.jpeg)

I would like to import also \*flt files in 3dslicer. Is that possible?

Thank you very much.

---

<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:** [November 20, 2017, 5:59pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/2 "2017-11-20T17:59:09Z")

</div>

See this thread: [Unable to do 3D rendering from a sequence of tiff images](https://discourse.slicer.org/t/unable-to-do-3d-rendering-from-a-sequence-of-tiff-images/1345/3)

---

<div class="post-metadata">

**Author:** ![laura\_rodriguez](https://avatars.discourse-cdn.com/v4/letter/l/e495f1/32.png) [@laura\_rodriguez](https://discourse.slicer.org/u/laura_rodriguez)\
**Post date:** [November 20, 2017, 7:03pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/3 "2017-11-20T19:03:57Z")

</div>

I have done all that, if you have a look to the first image you can see single file bottom is uncheck. In Volume menu, they appear each one of the images separately and not building a volume.

Any idea?

---

<div class="post-metadata">

**Author:** ![laura\_rodriguez](https://avatars.discourse-cdn.com/v4/letter/l/e495f1/32.png) [@laura\_rodriguez](https://discourse.slicer.org/u/laura_rodriguez)\
**Post date:** [November 20, 2017, 7:07pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/4 "2017-11-20T19:07:49Z")

</div>

Forget it, I only have to load one file, I was loading all of them…

Thank you for that.

I am continuing playing with the software

L

---

<div class="post-metadata">

**Author:** ![CRISTIAN\_ARMANDO\_HER](https://avatars.discourse-cdn.com/v4/letter/c/db5fbb/32.png) [@CRISTIAN\_ARMANDO\_HER](https://discourse.slicer.org/u/CRISTIAN_ARMANDO_HER)\
**Post date:** [November 28, 2017, 1:30pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/5 "2017-11-28T13:30:38Z")

</div>

Hello Laura,

I have the same problem for to load tiff images, but I don’t understand the instructions. Have I to load only a image? then how the volume is building with only a image?

Please, can you explain me how to do that it works?

---

<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:** [November 28, 2017, 1:53pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/6 "2017-11-28T13:53:56Z")

</div>

What did you do? What did you expect to happen? What happened instead?

---

<div class="post-metadata">

**Author:** ![CRISTIAN\_ARMANDO\_HER](https://avatars.discourse-cdn.com/v4/letter/c/db5fbb/32.png) [@CRISTIAN\_ARMANDO\_HER](https://discourse.slicer.org/u/CRISTIAN_ARMANDO_HER)\
**Post date:** [November 28, 2017, 2:22pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/7 "2017-11-28T14:22:21Z")

</div>

Hello,  
I have the tiff images of a CT Scan. I tried to load the images but the volume is not building, the images appears isolated. So I tried to follow this instructions: [https://www.slicer.org/wiki/Documentation/4.6/FAQ#How\_to\_load\_data\_from\_a\_sequence\_of\_jpg.2C\_tif.2C\_or\_png\_files.3F](https://www.slicer.org/wiki/Documentation/4.6/FAQ#How_to_load_data_from_a_sequence_of_jpg.2C_tif.2C_or_png_files.3F)  
If I understand the step 2, only a image need to be load. But when I do that only can see that slice.

Thanks

---

<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:** [November 28, 2017, 3:03pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/8 "2017-11-28T15:03:51Z")

</div>

Have you performed this step? “Click on Show Options and uncheck the Single File option”

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 26, 2020, 8:29pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/9 "2020-12-26T20:29:33Z")

</div>

I have done this, but just like cristian, I can only view one image. How can i see the full 3d volume? I have also followed all of the suggested steps above.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/d/4d3018c65bc2ce334afc0d69bd6329a8b3a9537a.png)

---

<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:** [December 26, 2020, 8:32pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/10 "2020-12-26T20:32:43Z")

</div>

You do have a volume, but since it came from a non-medical image format the default spacing of 1mm is used. You need to find out the correct spacing values and type them into the boxes.

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 26, 2020, 10:29pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/11 "2020-12-26T22:29:26Z")

</div>

I don’t understand … I did as you said, but it still isn’t displaying it correctly:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/a/4a42642b5c81f22ec48a3c9d05fc93c7d231a0d5.jpeg)

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [December 26, 2020, 10:32pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/12 "2020-12-26T22:32:03Z")

</div>

What do you want to see? All three planes are now visible, use the slides above each slice view to navigate different slices.  
Do you want to use 3D view? If so, you will need to use the Volume Rendering module.

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 26, 2020, 10:34pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/13 "2020-12-26T22:34:50Z")

</div>

I do want to see the 3d view, so how would I use the volume rendering module to create it? Btw thank you guys so much for you help!

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [December 26, 2020, 10:44pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/14 "2020-12-26T22:44:19Z")

</div>

> **[Volume rendering — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/user_guide/modules/volumerendering.html)**

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 26, 2020, 11:21pm UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/15 "2020-12-26T23:21:40Z")

</div>

The documentation was very helpful. However, I still have some problems. Do you know what I may do to make the 3d visualization more clear?

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/2/925ceb819042ae948667324ac6f3c9dca9abb25b.jpeg)

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [December 27, 2020, 12:10am UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/16 "2020-12-27T00:10:57Z")

</div>

This looks like a clinical CT scan, for which presets provided in the volume rendering module works reasonably well. Did you try chest CT? You can also use the Shift slider left and right to see if you can improve the visualization.

---

<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:** [December 27, 2020, 1:41am UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/17 "2020-12-27T01:41:30Z")

</div>

@Sarang_Goel please write a bit about your overall goal. You can get much more relevant answers much quicker if we know what you would like to achieve.

What anatomy and disease you are interested in? What is the clinical question you would like to get answered? What kind of visualization, processing, or analysis do you think would help you?

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 27, 2020, 1:43am UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/18 "2020-12-27T01:43:02Z")

</div>

So I have tried chest CT, but I am continuously getting the body with the image. However, I just want the lung. If I move the slider, the body does disappear, but so does the lung, leaving only the rib cage. Do you know what may I do?

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/9/d9433ddadf03e24460bf2ba54846b620bc26f323.jpeg)

---

<div class="post-metadata">

**Author:** ![Sarang\_Goel](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sarang_goel/32/9336_2.png) [@Sarang\_Goel](https://discourse.slicer.org/u/Sarang_Goel)\
**Post date:** [December 27, 2020, 1:44am UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/19 "2020-12-27T01:44:39Z")

</div>

So what my goal is to have the lung displayed, while simaltaneously dispalying a series of masked images (of abnormalities). It is centered around covid-19. These masks are already created and are also in tif format.

---

<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:** [December 27, 2020, 2:26am UTC](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494/20 "2020-12-27T02:26:32Z")

</div>

For covid lung visualizations, lung segmentation, and volumetric analysis you can use [Lung CT analyzer](https://discourse.slicer.org/t/new-lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006) extension. It is a Python scripted module so you can easily extend and customize it. We can also help making improvements or adding features, just let us know what you need.

[Next page](https://discourse.slicer.org/t/open-lung-ct-tiff-files/1494.md?page=2)