A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k
This PR introduces a way to smooth CSF and non-CSF tissues separately without propagation to minimize partial volume effect (PVE) arising from Gaussian filtering of voxels at the border.
Two methods have been currently introduced with one of them being default:
-cf or --csf_fsl using FSL FAST segmentation to derive a CSF mask
-cd or csf_adc n (default) using pseudo-ADC threshold of more than 2 (ADC > 2) to compute a CSF mask. Pseudo-ADC is defined as ln (S0/S1000) / (b1000/1000) . This method is flexible and looks for b-value shells close to 1000.
We found the latter method (2) to be more conservative and produce better results with minimal alteration of DTI/DKI metric while minimize PVE.
This PR introduces a way to smooth CSF and non-CSF tissues separately without propagation to minimize partial volume effect (PVE) arising from Gaussian filtering of voxels at the border.
Two methods have been currently introduced with one of them being default:
-cf or --csf_fslusing FSL FAST segmentation to derive a CSF mask-cd or csf_adc n(default) using pseudo-ADC threshold of more than 2 (ADC > 2) to compute a CSF mask. Pseudo-ADC is defined asln (S0/S1000) / (b1000/1000). This method is flexible and looks for b-value shells close to 1000.We found the latter method (2) to be more conservative and produce better results with minimal alteration of DTI/DKI metric while minimize PVE.