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carpentries-incubator / SDC-BIDS-dMRI

Introduction to dMRI
https://carpentries-incubator.github.io/SDC-BIDS-dMRI/
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vol_idx is a 1D-array containing the index of the first b0 #245

Closed AkhilaPhenomx closed 7 months ago

AkhilaPhenomx commented 8 months ago

Hi Team, I am exploring Diffusion data and came across your repository and trying to replicate it with the sample data I have. I didn't understanstand below step.

# vol_idx is a 1D-array containing the index of the first b0 dwi_brain, dwi_mask = median_otsu(dwi_data, vol_idx=[0])

what is the value of vol_idx in Diffusion Preprocessing episode?

jhlegarreta commented 7 months ago

median_otsu is a method that will compute the brain mask (remove the skull) and will return the mask and the brainmasked diffusion data. vol_idx tells which index of the input diffusion data (4D) volume is used to compute the mask. In this case, it is the first volume, corresponding to the index [0], which holds the b0 image: https://github.com/dipy/dipy/blob/4249da1987bad74cdc6cf1f69977b3a7132e7af8/dipy/segment/mask.py#L126