Joining together data from two different MRI protocols

In summary: DCE and T1-maps - and you are trying to match their baselines in order to accurately calculate the concentration of the contrast agent in each voxel. It is important to understand the process of baseline normalization and how the T1 values were obtained from the T1-maps. I recommend reaching out to the MRI scientists for assistance in understanding these steps and troubleshooting any discrepancies you have observed. With a clear understanding of the data and the process, you will be able to accurately analyze the data and achieve your goal of calculating the concentration of the contrast agent.I hope this summary has been helpful to you. Best of luck with your analysis!
  • #1
ElijahRockers
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I should start by saying that, as a novice data analyst, I have very little experience with MRI physics, but I believe I understand the absolute fundamentals. Also, this post mostly concerns data analysis issues so might be better suited for some other signal processing forum, but I'm hoping someone knowledgeable about MRIs might be able to at least point me in the right direction.

Below is as much as I have been able to understand about the data, assuming it's correct.

I have been given two data sets, encompassing a total three hour contrast enhanced MRI scan. In the first ten minutes, a large quantity of 'DCE' scans are taken, with contrast injection taking place sometime after the first ten or eleven DCE samples. These ten or eleven samples are pre-injection, and thus used as a baseline.

This produces some signal intensity for each voxel, which we can convert to a T1 weighted volume using the following equation:

[tex] S = \frac{S_0 sin(\alpha) (1 - E_1) e^{-TE/T2}}{[1-E_1 cos(\alpha)]}[/tex]

This equation is taken from an older paper: Contrast in Rapid MR Imaging: T1- and T2-Weighted Imaging by Richard B. Buxton, et al, and was given to me by the MRI scientists responsible for designing the protocol. They have verified that this is an equation I need to use.

From what I've gathered so far by talking to them:
  • since the TE value is very near 0, the equation simplifies.
  • [itex]S_0[/itex] for a given voxel is the average value of the DCE values there, pre-injection.
So, the remaining data set is not DCE, but standard 'T1-maps' (whatever the difference is between DCE and T1-maps I am still not entirely sure..., apparently each T1-map value is actually a value derived from 5 different scans with different flip angles, but I was not told how this was done) and supposedly the above equation can help me transform the DCE data into T1-maps, thereby allowing me to join the two data sets.

A T1-map has been taken pre-injection ([itex]T_{1,0}[/itex])also, to aid me in adjusting the DCE-derived T1 values so the two data sets agree on the same baseline, but I have been given no instructions on how to do this, and the MRI scientists appear uninterested in helping me understand how to process this data.

Once I have the entire data set in agreement on units and normalized to the correct baseline, I can calculate the concentration of the contrast agent in each voxel, which is what I'm really trying to get at here.

I have tried two different linear transformations to match the baselines but neither have been correct, and I am not sure if this baseline normalization is even supposed to be a linear transformation or not. After everything is said and done, the curve is supposed to appear smoothly decreasing, but there is a definite discontinuity between the DCE-derived T1 values and the T1-maps.

Perhaps there is something I am completely missing here, I welcome any suggestions at this point.
 
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  • #2

Thank you for sharing your concerns and questions regarding your data analysis for the MRI scan. As a scientist with experience in MRI physics, I would be happy to offer some guidance and point you in the right direction.

Firstly, I want to commend you for taking the initiative to understand the fundamentals of MRI physics, even though you are a novice data analyst. This will definitely help you in your analysis.

Based on the information you have provided, it seems like you have been given two types of data sets - DCE and T1-maps. DCE stands for Dynamic Contrast Enhanced, which means that these scans were taken after the injection of a contrast agent. T1-maps, on the other hand, are taken before the injection and are used as a baseline for comparison.

The equation you have been given is used to convert the signal intensity (S) obtained from the DCE scans to a T1-weighted volume. This equation takes into account the flip angle (alpha), the relaxation time (T1) and the echo time (TE). Since the TE value is close to 0, the equation simplifies.

The S0 value for a given voxel is the average value of the DCE scans before the injection. This value is used as a baseline for comparison with the T1-maps.

I understand that you are trying to match the baselines of the two data sets, but you have not been given clear instructions on how to do this. I would suggest reaching out to the MRI scientists responsible for designing the protocol and asking for their assistance in understanding the process of baseline normalization. It is important to have a clear understanding of this step in order to accurately calculate the concentration of the contrast agent in each voxel.

In terms of the T1-maps, the values you have been given are derived from 5 different scans with different flip angles. This is a common method used to obtain T1 values, known as variable flip angle method. The exact process of how these values are obtained may vary depending on the specific protocol used, so it would be best to ask the MRI scientists for more information on this.

In terms of the discontinuity you have observed between the DCE-derived T1 values and the T1-maps, it is possible that there may be some errors in the data or in your calculations. Again, I would suggest seeking assistance from the MRI scientists or other experts in the field to help troubleshoot and understand the discrepancy.

In
 

1. What is the purpose of joining together data from two different MRI protocols?

The purpose of joining together data from two different MRI protocols is to combine information from multiple images to gain a better understanding of the patient's condition. It allows for a more comprehensive analysis and can provide more accurate diagnostic information.

2. How is data from different MRI protocols joined together?

Data from different MRI protocols can be joined together using specialized software that aligns and blends the images. This process is called image registration and it involves matching corresponding points in the two images to create a single, merged image.

3. What are the benefits of joining together data from two different MRI protocols?

Joining together data from two different MRI protocols provides a more complete and detailed view of the affected area. It can also improve the accuracy of diagnosis and help in treatment planning. Additionally, it can save time and reduce costs by avoiding the need for multiple scans.

4. Are there any challenges in joining together data from two different MRI protocols?

Yes, there are some challenges in joining together data from two different MRI protocols. It requires advanced software and expertise to accurately register and blend the images. There may also be differences in image quality and resolution between the two protocols, which can affect the merging process.

5. Is it common for different MRI protocols to be used in one patient?

Yes, it is common for different MRI protocols to be used in one patient. Different protocols may be used to capture different types of information, such as structural, functional, or metabolic data. Combining data from these protocols can provide a more comprehensive view of the patient's condition.

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