How to change aslprep mask

1

Hello @tsalo,

We are processing pcasl with aslprep (0.7.0) and freesurfer preexisting outputs. We wonder whether the mask to segment the cbf according to tissue type is coming from freesurfer or fast. Besides, which threshold is applied to this mask. We have seen in the apply_mask0 it says threshold 0.5, and we were wondering whether we could do anything to apply a higher threshold.
If not possible, we would like to apply erode to the mask to improve tissue segmentation. Which aslprep output do we have to erode in that case?

Thank in advance!

2

ASLPrep uses sMRIPrep for the anatomical processing. I believe it uses FAST to produce the tissue type maps.

You can’t apply a higher threshold within ASLPrep, but you can definitely apply whatever tissue type masks you want to extract CBF by tissue type using the ASLPrep derivatives.

You could probably take the tissue type maps produced by ASLPrep and threshold them with the threshold you want, then apply binarized versions to mask the CBF outputs.