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.kom...@dkfz-heidelberg.de> 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:sthir...@ualberta.ca] > *Gesendet:* Samstag, 19. August 2023 04:42 > *An:* mitk-users@lists.sourceforge.net > *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* >
_______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users
