My ultimate goal is to obtain diffusion metrics between two ROI masks that are registered to subject native space. As of now, I am just preprocessing and setting up a pipeline using 10 subjects. I am following this tutorial GitHub - jjmcfadyen/hcp-diffusion-dcm: Scripts used in Experiment 2 of my PhD, using tractography and DCM on the HCP dataset
So far I have applied the following commands:
1. dwidenoise
2. dwifslpreproc
3. dwi2mask
4. dwibiascorrect ants
5. dwit2tensor
6. dwi2metric
7. dwinormalise group
Results from each command look accurate including the WM_mask output, however, the FA_Template.mif file is a white/empty image.
using mrinfo:
************************************************
Image name: "FA_template.mif"
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Dimensions: 109 x 127 x 97
Voxel size: 1.70312 x 1.70312 x 1.7
Data strides: [ -1 2 3 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 0 -88.45
0 1 0 -89.56
0 0 1 -67.01
command_history: /usr/local/pyenvs/versions/miniconda3-latest/envs/mrtrix3_fsl/bin/dwinormalise group -scratch /ifs/MRTRIX/tmpDIR/ -nthreads 12 -info -force /ifs/MRTRIX/OUTPUT//cDWI /ifs//MRTRIX/OUTPUT//BrainMasks /ifs/MRTRIX/OUTPUT//Normalised FA_template.mif WM_mask.mif (version=3.0.2)
mrtrix_version: 3.0.2
I am not sure where/what went wrong. Advice appreciated.