# How to analyze DCE-MRI data

**URL:** <https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622>\
**Category:** Support\
**Tags:** mri, dce, quantitative\
**Created:** [July 4, 2017, 7:49pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622 "2017-07-04T19:49:43Z")\
**Posts on this page:** 16\
**Page:** 3

<div class="post-metadata">

**Author:** ![speled](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/speled/32/1554_2.png) [@speled](https://discourse.slicer.org/u/speled)\
**Post date:** [May 15, 2018, 2:29pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/41 "2018-05-15T14:29:29Z")

</div>

@kirezgik, @fedorov - so what is the problem? PK Modeling works for me with this data set.  
What does not work is the “Output Fitted Data 4D” feature.

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [May 17, 2018, 6:12pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/42 "2018-05-17T18:12:48Z")

</div>

> [@speled](#):
>
> PK Modeling works for me with this data set.

I did not realize this was the case. What AIF did you use?

---

<div class="post-metadata">

**Author:** ![speled](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/speled/32/1554_2.png) [@speled](https://discourse.slicer.org/u/speled)\
**Post date:** [May 17, 2018, 6:30pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/43 "2018-05-17T18:30:56Z")

</div>

Hi – sorry I was not aware that the frame time issue had been figured out (since it was not brought up when we discussed Andrew and Jihun’s mouse data).

Attached is the AIF label map that I used – voxels found using an automated algorithm applied to an artery.

Best

Sharon

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [July 6, 2018, 3:04pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/44 "2018-07-06T15:04:01Z")

</div>

3 posts were split to a new topic: [DCE analysis - Fitted signal curve does not make sense](https://discourse.slicer.org/t/dce-analysis-fitted-signal-curve-does-not-make-sense/3403)

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [July 6, 2018, 3:00pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/47 "2018-07-06T15:00:23Z")

</div>

A post was split to a new topic: [DCE analysis - Ktrans is calculated only in a single small points](https://discourse.slicer.org/t/dce-analysis-ktrans-is-calculated-only-in-a-single-small-points/3402)

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 10, 2018, 2:44pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/48 "2018-08-10T14:44:07Z")

</div>

A post was merged into an existing topic: [How can I display the rCBV map acquired by DSCMRIAnalysis as a colormap?](https://discourse.slicer.org/t/how-can-i-display-the-rcbv-map-acquired-by-dscmrianalysis-as-a-colormap/3589/5)

---

<div class="post-metadata">

**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 14, 2018, 2:35am UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/49 "2018-08-14T02:35:17Z")

</div>

Dear Dr Fedorov,  
Hello again!  
I am using pkModeling module on a liver tumor analysis project.  
I have a question, that on [Huang2014](https://www.sciencedirect.com/science/article/pii/S1936523314800193), it says pkModeling(BWH-3DSlicer) is using Tofts model. The paper was published 4 years ago.  
I would like to make sure whether there is a upgraded model (for example Extended Tofts Model, or FXR-SSM) that is used in Slicer 4.9.0 nightly build version.  
The question come up in my mind, because on [this paper](https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.21066), it gives different definititions,  
[Tofts model Huang14]=[Kety model Parker06]  
[Extended Tofts model Huang14]=[Tofts model Parker06]  
which confused me.  
Thank you so much everytime!

–Tiger Hu

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 14, 2018, 1:57pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/50 "2018-08-14T13:57:23Z")

</div>

Tiger, we did not add any new models to PkModeling since the Huang2014 paper.

---

<div class="post-metadata">

**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 14, 2018, 3:25pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/51 "2018-08-14T15:25:46Z")

</div>

Dear Dr Fedorov,  
Since there is an option of computing fpv(i.e vp) with 3-parameter model,  
 ![%E5%9B%BE%E7%89%871](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/5/85d4956b0c3fdb9e13ad391994101f481264ad57.png)  
I assume you are using extended Tofts model, not Kety model  
 ![%E5%9B%BE%E7%89%872](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/2/e22eaf3c4ddfc356a928e3e9eaea43112c644158.png)  
because extended Tofts model contains 3 parameters Ktrans, vp and ve, and Kety model only contains 2.  
I will double check the results from calculation with pkmodeling module.  
Thanks again!  
-Tiger Hu

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 14, 2018, 4:42pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/52 "2018-08-14T16:42:50Z")

</div>

Both of those models (with and without fpv) were present at the time of the analysis reported in the Huang2014 paper, I think we just included one of those in the paper.

---

<div class="post-metadata">

**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 15, 2018, 1:16am UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/53 "2018-08-15T01:16:01Z")

</div>

Dear Dr Fedorov,  
Thank you for making it clear!

-Tiger Hu

---

<div class="post-metadata">

**Author:** ![KHATRINA](https://avatars.discourse-cdn.com/v4/letter/k/58f4c7/32.png) [@KHATRINA](https://discourse.slicer.org/u/KHATRINA)\
**Post date:** [December 20, 2018, 6:07pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/54 "2018-12-20T18:07:50Z")

</div>

> [@kirezgik](#):
>
> Actual behavior: Is there a way to do the quantitative [Torrent](https://downloader.vip/torrent-sites/)[TurboTax](https://downloader.vip/turbotax/) [Gogoanime](https://downloader.vip/gogoanime/) analysis of DCE MRI of pancreatic tumor? I can only do semiquantitative analysis and create the plotting chart which shows the time-signal intensity curves of different ROIs, as it is discussed in this tutorial:

Actual behavior: Is there a way to do the quantitative analysis of DCE MRI of pancreatic tumor? I can only do semiquantitative analysis and create the plotting chart which shows the time-signal intensity curves of different ROIs, as it is discussed in this tutorial:

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [December 20, 2018, 7:08pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/55 "2018-12-20T19:08:51Z")

</div>

> [@KHATRINA](#):
>
> Is there a way to do the quantitative analysis of DCE MRI of pancreatic tumor?

Yes, you can use the [PkModeling extension](https://www.slicer.org/wiki/Documentation/Nightly/Modules/PkModeling) for pharmacokinetic analysis of DCE

---

<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [November 21, 2019, 5:45pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/60 "2019-11-21T17:45:40Z")

</div>

3 posts were split to a new topic: [PkModeling tutorial](https://discourse.slicer.org/t/pkmodeling-tutorial/9257)

---

<div class="post-metadata">

**Author:** ![ThymusTheTrain](https://avatars.discourse-cdn.com/v4/letter/t/c0e974/32.png) [@ThymusTheTrain](https://discourse.slicer.org/u/ThymusTheTrain)\
**Post date:** [October 21, 2023, 10:17pm UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/63 "2023-10-21T22:17:04Z")

</div>

I tried following the tutorial linked in the OP, but after I load the test data I am unable to select anything for the Input Multivolume. I am using Slicer 5.

Could someone please guide me on how to properly load the data?

 ![DCE_Slicer_1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/9/191c850fa3c7658747decbec4ffa521e855393ab.png)  
 ![DCE_Slicer_2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/2/723fd7c8f84490e8a6fc47d3439e8f58f74e710e.jpeg)

---

<div class="post-metadata">

**Author:** ![smati\_wissem](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/smati_wissem/32/68776_2.png) [@smati\_wissem](https://discourse.slicer.org/u/smati_wissem)\
**Post date:** [January 11, 2024, 11:41am UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/64 "2024-01-11T11:41:11Z")

</div>

How can I extract the AIF mask, please

[Previous page](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622.md?page=2)