Hi @fedorov, I was wondering if you have any updates regarding to this issue.
@kirezgik no, unfortunately we do not have any new results. @speled and @mschwier did not identify the issue at the project week, and I have not been able to make time to investigate this myself. I am sorry!
Are you a developer yourself? Would you be comfortable investigating this issue? We could perhaps give you some pointers?
Hello @kirezgik, (cc: @fedorov,@mschwier)
The issue is probably not in the PK Modeling module, but in the multivolume loading of Bruker data - specifically in recognition of the frametime. I will probably be working on correcting this during Project Week in June. I do not have your problematic original data anymore - if you share it I think I can send you a solution.
all best
Sharon
Hi, I am not a developer myself, so I`d appreciate your help for that. @speled I just shared the original data with you.
Thanks,
Ezgi
@kirezgik (cc: @fedorov)
After you load the multivolume data, and save it (e.g. as .nhdr and .raw.gz) look at this field:
MultiVolume.FrameLabels:=0.0,9074472.1875,18148944.375,27223416.5625,…
This is a list of 90 values, and here it looks like the frametime is 9074472.1875 milliseconds, i.e. 151 minutes!
The frametime is usually in the range of 1-8 seconds…
Here’s how to correct this manually in the .nhdr file.
In the Slicer Dicom browser, highlight your DCE dataset and click the ‘metadata’ button at the bottom. You will see these fields:
0018,0080 RepetitionTime 65.64288
0018,0089 NumberOfPhaseEncodingSteps 96
Usually, the frametime in 2D sequences is the Repetition Time multiplied by the phase encoding steps. In this case that would be 6.3017 seconds.
So you should replace the FrameLabels list in the .nhdr file by 0,6301.7,etc…
Here is a Matlab script that generates the new list:
TR=65.6429;
numtimepoints=90;
PE=96;
%-----
framelabels=[0:TRPE:TRPE*(numtimepoints-1)];
newstring=sprintf(’%0.3f,’,framelabels);
% take off final comma…
newstring=newstring(1:end-1)
Let me know how this works for you?
all best
Sharon
@speled the issue of temporal resolution has already been discussed - see this post: How to analyze DCE-MRI data. That did not help.
@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.
I did not realize this was the case. What AIF did you use?
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
A post was merged into an existing topic: How can I display the rCBV map acquired by DSCMRIAnalysis as a colormap?
Dear Dr Fedorov,
Hello again!
I am using pkModeling module on a liver tumor analysis project.
I have a question, that on Huang2014, 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, 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
Tiger, we did not add any new models to PkModeling since the Huang2014 paper.
1 Like
Dear Dr Fedorov,
Since there is an option of computing fpv(i.e vp) with 3-parameter model,
I assume you are using extended Tofts model, not Kety model
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
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.
Dear Dr Fedorov,
Thank you for making it clear!
-Tiger Hu
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: