Calculation of T2 maps

[FroylanZR]

Hi Serena,

Im using my own set of images and am in the relaxometry step. Right now i only had one data set of the studies, so im not sure if the 3D map i got is accurate. I used the following files in my image_list_relaxometry_EP.txt file:

./preprocessed
./segmented
i1 01_S1T2_orig.mha
i2 01_S1T2_prep.mha
cm 01_S1T2_prep_fc.mha

[sbonaretti]

Hi!

I am finally back to full internet connection - thanks for your patience!

To calculate relaxometry maps (T2 or T1rho) you should use only *_orig.mha images because they contain the original image intensities (relaxometry maps are calculated from image intensities).
*_prep.mha images contain standardized intensities to favor segmentation, thus they should not be used to calculate relaxometry maps.
In addition, *_orig.mha and *_prep.mha images have the same mask (*_prep.fc.mha), because they went through the same spatial preprocessing, i.e. they have the same image orientation (RAI), origin (0,0,0) and laterality (left). So it correct to use *_prep_fc.mha also for *_orig.mha images

To calculate the relaxometry maps with pyKNEEr you need specific image sequences. To calculate:

• T2, you need a DESS acquisition, which contains 2 images acquired in the same acquisition
• T1rho, you need a cubeQuant acquisition, which contains 4 images acquired in the same acquisition

What kind of images are you using?

[FroylanZR]

Hi Serena,

We am currently using T2 images and trying to get optimal T1rho images to work with as well.

We are starting a new Knee project and we have a Siemens Vida in house with these sequences. We do not have T1rho.

• T2, you need a DESS acquisition, which contains 2 images acquired in the same acquisition
o We have Siemens Knee Cartilage: 3D DESS 160 slices; 0.60 mm [t2_de3d_we_sag_iso]
• T1rho, you need a cubeQuant acquisition, which contains 4 images acquired in the same acquisition
o Can we use this? T2*-weighted 3D Multi-Echo Data Image Combination [t2_me3d_we_sag_iso]

any feedback would be appreciated! thanks!

[sbonaretti]

Hi,

I am not familiar about your image acquisition protocols, so I unfortunately cannot give you much of a feedback. But here are some information related to what I used, so maybe you can find similarities and differences with your protocols:

• pyKNEEr's paper: at page 9, paragraph "Cartilage relaxometry" you can see how I calculated the maps
• Linear fitting paper: describing the exponential fitting and the acquisition protocols of the used images
• EPG paper: describing calculation of T2 maps from DESS images using Extended Phase Graph (EPG) modeling and the acquisition protocols of the used images

Hope this can be of help!