Dear all,
I am interested in performing Fixel based analysis with single shell data.
I have noticed that there are four pipelines mentioned in mrtrix/readthedocs and mrtrix community for data pre-processing before FOD estimation.
1. First pipeline can be found here
http://mrtrix.readthedocs.io/en/latest/workflows/DWI_preprocessing_for_quantitative_analysis.html and brings the title “DWI Pre-processing for Quantitative Analysis”. The steps outlined in this pipeline are the following:
- DWI denoising
- DWI preproc
- Brain mask estimation
- Bias field correction
- Global intensity normalisation across subjects
- Computing a group average response function
2. Second pipeline can be found here
http://mrtrix.readthedocs.io/en/latest/workflows/fixel_based_analysis.html and brings the title “Fixel-Based Analysis (FBA)”. The steps outlined in this pipeline are the following:
- Upsampling DW images
- Compute upsampled brain mask images
- Fibre Orientation Distribution estimation
…
3. Third pipeline can be found here
http://mrtrix.readthedocs.io/en/latest/tutorials/basic_dwi_processing.html and brings the title “Basic DWI processing”. The steps outlined in this pipeline are the following:
- DWI preproc
- Brain mask estimation
- Response function estimation
- Fibre Orientation Distribution estimation
…
4. Fourth pipeline can be found here Single-shell data. The steps outlined in this pipeline are the following:
-Upsample your dMRI to the same isotropic resolition of your sMRI
-Preprocessing your diffusion data (eddy correction, bias, etc…)
-Co-register your strucural data to the diffusion
-Correct for distortion using restricted registration (this option is implemented in ANTs, with the option -g). Take a look to this paper4 and this one3 for more details.
-Now booth images are aligned, if do you think that the alignement is good, you can perform ACT.
In my effort to unify the above I ended up with the following pipeline:
- Denoising
- Upsampling
- Preproc (for eddy only, no topup)
- Brain mask extraction
- Bias field correction
- Global intensity normalisation across subjects
- Group average response function estimation
- Structural and diffusion data co-registration
- Distortion correction using restricted registration (this option is implemented in ANTs, with the option -g).
- Fibre Orientation Distribution estimation
- Study-specific unbiased FOD template generation
- Registration of all subject FOD images to the FOD template
- Computation of intersection of all subject masks in template space … next steps as listed in the FBA page
Could you please let me know if you would rearrange/amend/delete any of the above processes or whether you would add any?
Do you also might have a specific command-line/ link for the following step: Correct for distortion using restricted registration (this option is implemented in ANTs, with the option -g)?
Cheers,
Vasiliki