Re: [mitk-users] [Extern] - Help with DCE MR Perfusion Datafit view

[Sibi T. <sth...@ua...>]

Thanks, Ina, that worked.

I do have a follow-up question. I am trying to do a two-compartment
exchange model for Blood-brain barrier permeability calculation using DCE
CT. I am not able to find the concentration conversion factor K for DCE CT.
Do I have to go with a reference value for this? or this can be calculated
from the imaging data as well?

Best

Sibi

On Mon, Aug 21, 2023 at 2:01 AM Kompan, Ina Nora <
i.k...@dk...> wrote:

> Dear Sibi,
>
>
>
> it looks like the mask of your region of interest is (at least partially)
> not within the image region which is processed during the fitting. How have
> you created the mask? Have you generated it in MITK?
>
>
>
> If you haven’t done so yet I would recommend trying the following steps:
>
> 1)      Open your 4D DCE CT image in the Data Manager.
>
> 2)      Open the segmentation plugin with the DCE CT image as input and
> select a new segmentation (+ button).
>
> 3)      In the pop-up window select “Create static segmentation”.
>
> 4)      Use the segmentation tools at the bottom of the plugin to create
> the mask in one of the time steps (for a static segmentation the mask will
> be the same for all time steps).
>
> 5)      The mask will appear as a sub-node of the DCE CT data in the Data
> Manager. To avoid confusion, you can rename the mask in the Data Manager,
> e.g. to “Tumor-label”.
>
> 6)      If you are using a model that requires an arterial input
> function, you can repeat the steps for the segmentation of an AIF mask.
>
> 7)      In the DCE MR Perfusion Datafit View, set the ROI mask (and AIF
> mask if used) as input.
>
>
>
> You can also find a detailed documentation on segmentation in MITK when
> you press F1 when the segmentation plugin is active (the tab of the plugin
> is highlighted).
>
>
>
> I hope this helps.
>
>
>
> Best wishes,
>
> Ina
>
>
>
>
>
>
>
> *Von:* Sibi Thirunavukkarasu [mailto:sth...@ua...]
> *Gesendet:* Samstag, 19. August 2023 04:42
> *An:* mit...@li...
> *Betreff:* [Extern] - [mitk-users] Help with DCE MR Perfusion Datafit view
>
>
>
> Dear all, I am trying to calculate blood-brain barrier permeability using
> DCE CT. When I try to run the DCE MR Perfusion DATA fit view using
> pixel-based fitting strategy, I encounter the following error.
>
>
>
> *MultiOutputNaryFunctorImageFilter(000001C623DA28F0): Mask of filter is
> set but does not cover region of thread. Mask region: ImageRegion
> (000001C6119AB2C0) Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 16]
> Thread region: ImageRegion (000000C40EDFEB70) Dimension: 3 Index: [0, 0, 0]
> Size: [512, 516, 1] *
>
> *Fitting finished.*
>
>
>
> *I am not sure how to proceed further to rectify this error. *
>
>
>
> *Best regards*
>
>
>
> *Sibi*
>