Access intensity Values from Time intensity plots in Quantiphyse

[XJGB]

Hi everyone,

First of all Thanks so much for providing such a well organized and easy to understand and well documented tool for quantitative MRI data analysis.

Is there currently an in built functionalty to access ROI based intensity values of a 4D-dataset?

So far i have only been able to access mean intensity which is not what i want.

Thanks for your help!

best Regards
Florian

[mcraig-ibme]

Hi, apologies, I'm not completely sure what you are after - could we just clarify?

You have a 4D dataset and an ROI, so for each voxel in your ROI there is a time series of values. Do you want to be able to extract these values for a particular voxel? Or for all voxels in the ROI? If it is the latter, what format would you want the output to appear in?

I suspect we don't have what you're looking for immediately built in but it might be possible to either add it easily or get the information from existing tools.

Thanks, Martin

[XJGB]

Hi - thanks for your reply! Sorry if my request was not very clear!

I have 4D Datasets in nifti format ROIs are also in nifti format as I have generated them in quantiphyse! Primary goal is to analyse these with the Bayesian DCE module. Currently however we still have trouble with our AIF.

So i'd like to access DCE data as time/intensity curves of different ROIs in order to get a first preliminary impression of the Data.

As a work-around I did this so far using the AIF-widget, which provides the SI-values over time within my ROI.
As I have several ROIs this is doable but a bit unhandy.

I was just wondering if there was a smarter, more efficient way to access these Data?

In general and for the future: would it be possible to analyse larger Sets of 4D-Data with matching ROIs using the Bayesian DCE functionality of quantiphyse for example on a command line base?

Thanks for your help! Best regards
Florian

[XJGB]

oh and i forgot to mention: I would like to have the intensity values as a mean of the Voxels within the ROI

[mcraig-ibme]

Thanks Florian. I'm not sure we have something to do quite what you want at present - although it would not be difficult to extend the AIF widget to accept a multi-value ROI and generate multiple AIF curves in response. If I understand you correctly you would be looking for a way to do multiple runs of the DCE fitting using different AIFs, each corresponding to a different region in your ROIs?

The closest thing we have currently is the 'Mean in ROI' tool under Widgets->ROIs. This accepts a 4D dataset and a 3D multi-label ROI and generates a 4D dataset where the timeseries in each ROI is the mean timeseries for all voxels in that ROI. However there isn't an automatic way to write these timeseries out in a way that could be used as AIFs.

[XJGB]

Hi Martin,

thank you very much for your getting back to me and your help! Yes I was looking for the functionality as you described in the Mean in ROI tool - perfect!!
Sorry for the late reply!

In general i am looking for a way to analyze my DCE datasets in a more 'high-throughput'-fashion - and I was wondering if there was a way to use existing functionality of quantiphyse for that!

best Regards and thanks again!
Florian