Dear Mrtrix Experts,
I have an exvivo human spinal cord dataset. They are with 2 bva0 and 750, and 1500, each 12 directions. I’m trying to get a good response function in order to generate CSD map and Tractography. I would like to use Mrtrix 3 to do so.
I’ve used the dwi2response tournier , dhollander, fa and manual algorithm using the whole cord or only selecting for the single fibre orientation WM tract areas. I am still not satisfied about the outcome of response function. I think I should aim to get a response function close to a flat oblate shape in order to get a good FODs? Could you recommend if this can be better performed?
I have done the following steps:
A. response calculation using the whole cord mask

I converted the dicom to nifti format using (MIPAV) for first sample 3 shells b0,750 &1500. For second sample (b0&3000) I used mrconvert dwi2nifti

For the gradient table, I swapped the gradient from xyz to zyx (I used data that come from Bruker preclinical animal scanner)

Biasfield correction of the B0 using ANTS N4biascorrection, and applied this correction to the whole 4D DWI dataset

Then, I ran the following tests for each individual shell
AResponse function calculations using the “tournier” algorithm using a mask containing whole cord at bvalue 1500
dwi2response tournier < Input DWI> < Output response text file>
The above commands were repeated for the b=750.
I got this response function at b1500.
The response function values at b1500 are
16616.92061510039 3585.731063681506 662.1366725620043 49.21846975544766 372.193208900446 89.22703866558832
Also, I tested the TOURNIER algorithm on another sample with 2 shell (b0&3000). I got the following response function
The response function values at b3000 are 15261.69894075049 3513.609487088777 1043.844357488741 145.3679829867056 2.01888135870964 11.80721638417216
BResponse function calculations using the “tournier” algorithm using a mask containing selected voxels of SPINAL CORD WM AT bvalue 750 & 1500
The response function values at b750 are
24174.5778079981 1711.70084036846 442.5087763272201 13.27346114028632 12.25772995997397 58.66570209134966
here is the response function using the same algorithm at b1500
The response function values at b1500 are
9416.77124310872 1993.300817125692 211.8305534782687 85.78772928903967 89.50880832164782 54.91400798555078
*The other methods for response function result will be posted soon.
Many Thanks,
Hattan