Hello, mrtrix community! Long story short: dwi.mif and dwi_corr.mif after dwifslpreproc looks exactly the same in regard to the artefacts.
I am new to MRI data analysis and relatively new to using a command line. It is possible that I am missing a small detail.
I have a set of studies performed on a Siemens Skyra MAGNETOM 3T machine with a DTI (ep2d_diff_mddw_30_p2) sequence. To the best of my knowledge, my data is acquired in a single phase encoding direction A>>P with 30 directions of the diffusion gradient. I am working on mac under Mac OS 10.15.7. and mrtrix version 3.0.2.
My aim is to eventually perform a TBSS analysis of this data. This is my typical workflow:
- Convert dicom to .nii with MRIcron ignoring derived and 2D images. It leaves me with one DWI file and a set of .bvec and .bval and .json
- Convert .nii to .mif:
mrconvert dwi.nii dwi.mif -fslgrad dwi.bvec dwi.bval -json_import dwi.json
- Denoise with:
dwidenoise dwi.mif dwi_out.mif -noise noise.mif
- Running dwifslpreproc:
dwifslpreproc dwi.mif dwi_out.mif -rpe_header -eddy_options="–slm=linear"
I receive a warning:
[WARNING] DWI header indicates no phase encoding contrast between b=0 images; proceeding without inhomogeneity field estimation
and the process goes on. I do not know whether it is a crucial warning. The problem is that the output file I receive has the same alterations in the frontal lobes as the input file.
My understanding is that I have to use slm=linear due to direction of the diffusion gradient is less than 60. I am not sure about my readout time, as I have calculated it to be 48msec and mrinfo says it is 3.7:
Voxel size: 1.71875 x 1.71875 x 5.2 x 3.7
I also try to include as much information as I have into the .mif header. Should I specify anything else for dwifslpreproc to run correctly? As I am not allowed to attach files, I would provide mrinfo output in the comments upon your request.
Thanks in advance!