Is it possible to use dwi2response to estimate the response function from a small brain section?
The data I have is an approx 5x4x1cm section imaged in a pre-clinical scanner with b=5000 s/mm2.
With the tournier algorithm I get a response function:
However I am using fslgrad to specify the bvecs/bvals. Similar to other posts, does this shape suggest an error in the definition of the gradient table?
Thanks in advance for your help!
It’s difficult to tell from the shape of the response function alone, particularly with ex vivo data where the signal is not attenuated as strongly for a given b-value as is in vivo data.
If you have doubts about the handling of the gradient table information, see if the
dwigradcheck script provides any insight. If anything other than the baseline table (i.e. no axis flip, no permutations) results in the longest mean streamline length, try using the modified gradient table as selected by
dwigradcheck and re-running your processing.
Thanks so much for getting back to me - your advice is really helpful.
After investigating the gradient table information, I think you’re right that the issue is with the quality of the signal from the ex vivo data.