I am working on a project that has acquired DTI (in 64 directions) and DWI (in one direction at 4 b-values: b0 and three other values under 1200, based on previous literature--this paper did NOT use FSL to process the data). I am familiar with DTI analysis and this data is not a problem to analyze using FSL FDT Toolbox. However, I am having issues with the DWI data.
First, part of my confusion is nomenclature. I've seen numerous uses of ADC, diffusivity and Trace (D). I've also seen the following in a previous post:
"- ADC is defined along a single orientation (hence it is not L1+L2+L3).
- MD is the mean of ADC across all orientations (though, again, some people might use the terms interchangeably)
- The trace is L1+L2+L3 (math definition), hence MD=Trace/3."
Based on this I would like to create the ADC maps in the x, y, and z direction, an average of those maps (which I am assuming is the MD) and the Trace image (which I am assuming would be: MD*3=Trace OR L1+L2+L3). **Please correct me if my descriptions are incorrect.
If this is correct I could try to use the FDT Toolbox-DTIFIT to create the MD. In order to do this I would have duplicate the 4 volumes and append them to the original 4 volumes for a total of 8 volumes. I am making this assumption since DTIFIT require a minimum of 6 volumes to run (at least in my experience). Is this method appropriate?
If this method is okay, the FA map will essentially be binary (since the data was collected in only one direction), but the MD output should be correct. Yes/No?
If so, I should then be able to use fslmaths to multiply the MD by 3 and output the Trace image. Yes/No?
The ADC maps are then L1, L2, L3? Or does some calculation need to be made to generate these maps?
This method seems straight forward, if considered valid
***Alternatively, I could use the diffusion formula to calculate the ADC maps from the raw volumes since I have the b0 and the b-weighted images? Correct?
With the help of my colleague Yossi Berlow at OHSU I post these steps to manually determine the ADC:
S=signal with diffusion
So=signal without diffusion
D=-(1/b)ln(S/So)
rearranged
D=-(lnS-lnSo)/b
if b=1000
fslmaths S -log lnS
fslmaths So -log lnSo
fslmaths lnS -sub lnSo lnS_sub_lnSo
fslmaths lnS_sub_lnSo -div -1000 D
I should be able to implement this for each b-value, average the images together using fslmaths for the MD, and divide the MD by 3 to get the Trace? I don't know if the above steps are correct so please advise or if should be able to compare them to the output from DTIFIT. I've tried comparing results between the two methods to no avail, which leads me to believe that I am forgetting to do something (or many things)!!!
I apologize for the long post, but I appreciate any effort in helping with this issue
David
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