Update to below question: nipype has a watershed algorithm to segment given image into white and grey matter. I am not sure though how to use this API. https://github.com/nipy/nipype/search?utf8=✓&q=WatershedSkullStrip&type=
I provide a .nii file in the in_file parameter. On calling the
‘mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz’
nothing happens. How to use this WaterShedSkullStrip() API so that a segmented image is ouput ?
I have installed nilearn on my ubuntu 16.8 LTS. I am trying to implement some basic preprocessing steps to analyse abide datasets currently with the dparsf pipeline. I am wondering if nilearn has a way to segment the brain images into grey and white matter and compare the densities of these regions ?